attributes.tag: 16S rRNAs recovered
attributes.value: 0
attributes.tag: 16S recovered
attributes.value: FALSE
attributes.tag: 16S recovery software
attributes.value: barrnap;0.9;--kingdom bac
attributes.tag: 23S rRNAs recovered
attributes.value: 0
attributes.tag: 5S rRNAs recovered
attributes.value: 0
attributes.tag: CheckM strain heterogeneity
attributes.value: 100
attributes.tag: ENA first public
attributes.value: 2022-04-01
attributes.tag: ENA last update
attributes.value: 2022-04-01
attributes.tag: External Id
attributes.value: SAMEA13493338
attributes.tag: GTDB r202 classification
attributes.value: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans
attributes.tag: INSDC center alias
attributes.value: Stanford University School of Medicine
attributes.tag: INSDC center name
attributes.value: stanford university school of medicine
attributes.tag: INSDC first public
attributes.value: 2022-04-01T08:25:13Z
attributes.tag: INSDC last update
attributes.value: 2022-04-01T08:25:13Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: MAG coverage depth
attributes.value: 8.43
attributes.tag: MAG coverage software
attributes.value: Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
attributes.tag: Submitter Id
attributes.value: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_14_2337.66
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.
attributes.tag: assembly software
attributes.value: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz
attributes.tag: binning parameters
attributes.value: Reads from ERR7738269 were assembled into contigs (ERZ4559654). The following read sets from this study were the most similar to ERR7738269 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738269,ERR7745412,ERR7738185,ERR7745403,ERR7738166,ERR7738201,ERR7745388,ERR7738171,ERR7738159,ERR7737968. 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 ERZ4559654. 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.
attributes.tag: binning software
attributes.value: MetaBAT2 v2.15; MAGpurify v2.1.0
attributes.tag: collection date
attributes.value: 2014-08-14
attributes.tag: completeness approach
attributes.value: CheckM marker lineage: f__Lachnospiraceae (UID1256)
attributes.tag: completeness score
attributes.value: 88.94
attributes.tag: completeness software
attributes.value: CheckM;1.1.2;lineage_wf
attributes.tag: contamination score
attributes.value: 0.58
attributes.tag: contamination screening input
attributes.value: reads
attributes.tag: contamination screening parameters
attributes.value: All reads in ERR7738269 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).
attributes.tag: environment (biome)
attributes.value: terrestrial biome
attributes.tag: environment (feature)
attributes.value: human-associated habitat
attributes.tag: environment (material)
attributes.value: feces
attributes.tag: geographic location (country and/or sea)
attributes.value: Tanzania
attributes.tag: geographic location (elevation)
attributes.value: 1287
attributes.tag: geographic location (latitude)
attributes.value: -3.55
attributes.tag: geographic location (longitude)
attributes.value: -34.58
attributes.tag: inter-study species representative
attributes.value: GUT_GENOME000493
attributes.tag: intra-study species representative
attributes.value: ERR7737955_bin.14
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation source
attributes.value: human feces
attributes.tag: metagenomic source
attributes.value: human gut metagenome
attributes.tag: nucleic acid extraction
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: number of standard tRNAs extracted
attributes.value: 20
attributes.tag: project name
attributes.value: Metagenome sequencing of Hadza gut microbiome
attributes.tag: reassembly post binning
attributes.value: No
attributes.tag: reference for biomaterial
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: sample collection device or method
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: sample derived from
attributes.value: ERS2586207
attributes.tag: sample name
attributes.value: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_14_2337.66
attributes.tag: sequencing method
attributes.value: Illumina NovaSeq 6000
attributes.tag: tRNA extraction software
attributes.value: tRNAscan-SE;2.0.9;-B
attributes.tag: taxonomic classification
attributes.value: GTDB-TK v1.7.0, r202 database, default parameters
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach
attributes.tag: unique standard tRNAs extracted
attributes.value: 11