characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_C-REDO_D_2_1542.51

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745625 were assembled into contigs (ERZ4566938). The following read sets from this study were the most similar to ERR7745625 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745625,ERR7738227,ERR7738534,ERR7745854,ERR7745398,ERR7738957,ERR7745431,ERR7746345,ERR7745947,ERR7738606. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4566938. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745625 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Anaerostipes sp. MAG assembled and binned from ERR7745625.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Anaerostipes sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Anaerostipes sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


status: PUBLIC

tag: attribute

characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528.211

tag: Namespace:Stanford University School of Medicine

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738559 were assembled into contigs (ERZ4567799). The following read sets from this study were the most similar to ERR7738559 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738559,ERR7738239,ERR7746721,ERR7738586,ERR7746365,ERR7745815,ERR7746321,ERR7738614,ERR7738531,ERR7738561. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567799. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738559 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Anaerostipes sp. MAG assembled and binned from ERR7738559.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Anaerostipes sp.

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Anaerostipes sp.

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_P_14_2348.75

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746012 were assembled into contigs (ERZ4559707). The following read sets from this study were the most similar to ERR7746012 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746012,ERR7738267,ERR7738206,ERR7738233,ERR7738212,ERR7738461,ERR7738221,ERR7738256,ERR7738629,ERR7738244. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559707. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7746012 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Anaerostipes sp. MAG assembled and binned from ERR7746012.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Anaerostipes sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Anaerostipes sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_F_6_1630.56

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745582 were assembled into contigs (ERZ4561354). The following read sets from this study were the most similar to ERR7745582 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745582,ERR7738531,ERR7747083,ERR7745556,ERR7738552,ERR7745544,ERR7738957,ERR7738208,ERR7746365,ERR7738556. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561354. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745582 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Anaerostipes sp. MAG assembled and binned from ERR7745582.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Anaerostipes sp.

characteristic: organism

text: No

text: uncultured Anaerostipes sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525.38

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738660 were assembled into contigs (ERZ4567818). The following read sets from this study were the most similar to ERR7738660 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738660,ERR7738561,ERR7738251,ERR7746660,ERR7738614,ERR7738586,ERR7738228,ERR7738275,ERR7746321,ERR7738219. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567818. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: f__Lachnospiraceae (UID1256)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738660 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bariatricus sp. MAG assembled and binned from ERR7738660.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Bariatricus sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bariatricus sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp900539115

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_A_12_1112.95

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745425 were assembled into contigs (ERZ4561787). The following read sets from this study were the most similar to ERR7745425 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745425,ERR7745577,ERR7745588,ERR7745432,ERR7746094,ERR7738230,ERR7745759,ERR7746767,ERR7746440,ERR7745648. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561787. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745425 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7745425.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_L_24_2330.311

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745783 were assembled into contigs (ERZ4559670). The following read sets from this study were the most similar to ERR7745783 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745783,ERR7738263,ERR7745291,ERR7738193,ERR7738604,ERR7738243,ERR7746757,ERR7747255,ERR7745335,ERR7745990. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559670. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745783 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7745783.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Eubacterium sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307.48

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738605 were assembled into contigs (ERZ4567948). The following read sets from this study were the most similar to ERR7738605 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738605,ERR7738574,ERR7738629,ERR7738256,ERR7738221,ERR7746365,ERR7738461,ERR7738631,ERR7738569,ERR7746321. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567948. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738605 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7738605.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_B_21_1589.101

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738245 were assembled into contigs (ERZ4561113). The following read sets from this study were the most similar to ERR7738245 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738245,ERR7745434,ERR7738188,ERR7746184,ERR7738565,ERR7745919,ERR7738556,ERR7738651,ERR7738180,ERR7738531. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561113. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738245 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7738245.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Eubacterium sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_SUBJECT_CONTIGS_1500_ASSEMBLY_K77_MERGED__Pilot_MoBio_Fiber_C_21_7002.92

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738597 were assembled into contigs (ERZ4558864). The following read sets from this study were the most similar to ERR7738597 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738597,ERR7738562. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 2 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4558864. Depth information for all 2 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738597 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7738597.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: Metagenome sequencing of Californian gut microbiome

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_G_15_1738.191

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738536 were assembled into contigs (ERZ4560348). The following read sets from this study were the most similar to ERR7738536 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738536,ERR7738626,ERR7745823,ERR7738607,ERR7738613,ERR7738598,ERR7745990,ERR7745335,ERR7738936,ERR7745845. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560348. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738536 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7738536.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Eubacterium sp.

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_I_4_2616.197

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746111 were assembled into contigs (ERZ4559340). The following read sets from this study were the most similar to ERR7746111 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746111,ERR7738617,ERR7738261,ERR7738527,ERR7738664,ERR7745845,ERR7738569,ERR7738599,ERR7738577,ERR7745990. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559340. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7746111 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7746111.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315.120

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746349 were assembled into contigs (ERZ4568042). The following read sets from this study were the most similar to ERR7746349 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746349,ERR7738602,ERR7738628,ERR7738571,ERR7738552,ERR7745963,ERR7738587,ERR7745544,ERR7738557,ERR7738584. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4568042. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7746349 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7746349.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Eubacterium sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_G_3_1732.132

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738532 were assembled into contigs (ERZ4560754). The following read sets from this study were the most similar to ERR7738532 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738532,ERR7738577,ERR7738613,ERR7746051,ERR7747322,ERR7738936,ERR7738536,ERR7738595,ERR7738576,ERR7738607. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560754. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738532 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7738532.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_G_18_2610.229

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745823 were assembled into contigs (ERZ4559376). The following read sets from this study were the most similar to ERR7745823 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745823,ERR7747394,ERR7745335,ERR7738959,ERR7747255,ERR7746688,ERR7738598,ERR7745990,ERR7745947,ERR7746217. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559376. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745823 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7745823.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Eubacterium sp.

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_M_19_2499.111

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7747615 were assembled into contigs (ERZ4559937). The following read sets from this study were the most similar to ERR7747615 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7747615,ERR7738169,ERR7738145,ERR7738148,ERR7746344,ERR7745922,ERR7745948,ERR7738461,ERR7745675,ERR7738569. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559937. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7747615 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7747615.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: No

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp001414325

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640.378

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738628 were assembled into contigs (ERZ4567910). The following read sets from this study were the most similar to ERR7738628 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738628,ERR7738571,ERR7738602,ERR7746349,ERR7738531,ERR7738587,ERR7738208,ERR7738606,ERR7746365,ERR7746321. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567910. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738628 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738628.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp900759665

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ.65

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738433 were assembled into contigs (ERZ4567237). The following read sets from this study were the most similar to ERR7738433 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738433,ERR7738529,ERR7745755,ERR7738575,ERR7738580,ERR7745760,ERR7745858,ERR7738277,ERR7738258,ERR7738558. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567237. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738433 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738433.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: Metagenome sequencing of Nepali gut microbiome

text: No

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp001916135

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_K_24_1920.242

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746688 were assembled into contigs (ERZ4560553). The following read sets from this study were the most similar to ERR7746688 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746688,ERR7738260,ERR7747394,ERR7738586,ERR7745335,ERR7746321,ERR7738628,ERR7738959,ERR7738606,ERR7738599. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560553. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7746688 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7746688.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp003524945

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_D_13_1581.111

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7745433 were assembled into contigs (ERZ4561097). The following read sets from this study were the most similar to ERR7745433 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745433,ERR7746692,ERR7745411,ERR7738195,ERR7738200,ERR7738242,ERR7745362,ERR7738556,ERR7738574,ERR7746321. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561097. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745433 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7745433.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: No

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_K_13_1776.273

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738623 were assembled into contigs (ERZ4560388). The following read sets from this study were the most similar to ERR7738623 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738623,ERR7746433,ERR7738591,ERR7738598,ERR7738626,ERR7745823,ERR7738607,ERR7745335,ERR7738584,ERR7738557. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560388. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738623 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738623.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp000433735

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_N_5_1522.177

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746184 were assembled into contigs (ERZ4561544). The following read sets from this study were the most similar to ERR7746184 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746184,ERR7738610,ERR7738200,ERR7745815,ERR7738569,ERR7738586,ERR7747426,ERR7738608,ERR7738559,ERR7746321. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561544. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Clostridiales (UID1212)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7746184 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Eubacterium sp. MAG assembled and binned from ERR7746184.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Eubacterium sp.

characteristic: organism

text: No

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_G_1_1731.199

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738563 were assembled into contigs (ERZ4560756). The following read sets from this study were the most similar to ERR7738563 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738563,ERR7738936,ERR7738613,ERR7738595,ERR7738577,ERR7746048,ERR7738607,ERR7747140,ERR7746051,ERR7738569. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560756. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738563 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738563.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_K_3_2480.104

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738143 were assembled into contigs (ERZ4559842). The following read sets from this study were the most similar to ERR7738143 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738143,ERR7746779,ERR7738179,ERR7738608,ERR7747426,ERR7738569,ERR7738200,ERR7738610,ERR7738203,ERR7746184. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559842. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738143 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738143.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: No

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG14107;s__RUG14107 sp900772685

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530.144

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738531 were assembled into contigs (ERZ4567864). The following read sets from this study were the most similar to ERR7738531 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738531,ERR7747083,ERR7745556,ERR7738602,ERR7738552,ERR7745582,ERR7738628,ERR7745854,ERR7738565,ERR7738587. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567864. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: o__Clostridiales (UID1226)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738531 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738531.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774;s__UBA11774 sp003507655

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_SUBJECT_CONTIGS_1500_ASSEMBLY_K77_MERGED__Pilot_MoBio_Fiber_I_11_1003.293

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738665 were assembled into contigs (ERZ4558928). The following read sets from this study were the most similar to ERR7738665 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738665,ERR7738546. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 2 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4558928. Depth information for all 2 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: f__Lachnospiraceae (UID1255)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738665 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738665.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: Metagenome sequencing of Californian gut microbiome

text: No

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_N_21_1514.65

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745897 were assembled into contigs (ERZ4561483). The following read sets from this study were the most similar to ERR7745897 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745897,ERR7745565,ERR7746285,ERR7738152,ERR7738214,ERR7738184,ERR7745362,ERR7738200,ERR7738154,ERR7745903. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561483. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: f__Lachnospiraceae (UID1286)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745897 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7745897.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Lachnospiraceae bacterium

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach