ERR7738155_bin.39
collection_date
2014-06-16
assembly software
metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz
sample derived from
ERS2586078
contamination screening input
reads
geographic location (longitude)
-34.58
geographic location (elevation)
1287
number of standard tRNAs extracted
37
CheckM strain heterogeneity
0
ENA-FIRST-PUBLIC
2022-04-01T08:20:16Z
ENA-LAST-UPDATE
2022-04-01T08:20:16Z
completeness software
CheckM;1.1.2;lineage_wf
nucleic acid extraction
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
completeness approach
CheckM marker lineage: p__Firmicutes (UID1022)
GTDB r202 classification
d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Allisonella;s__Allisonella histaminiformans
binning software
MetaBAT2 v2.15; MAGpurify v2.1.0
inter-study species representative
GUT_GENOME192289
5S rRNAs recovered
2
organism
uncultured Allisonella sp.
sample collection device or method
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
scientific_name
uncultured Allisonella sp.
investigation type
metagenome-assembled genome
MAG coverage software
Reads (ERR7738155) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560511) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
metagenomic source
human gut metagenome
project name
Metagenome sequencing of Hadza gut microbiome
sequencing method
Illumina NovaSeq 6000
most complete 23S rRNA recovered
NA
23S rRNAs recovered
0
most complete 5S rRNA recovered
0.9327731092436975
reassembly post binning
No
16S rRNAs recovered
0
intra-study species representative
ERR7738155_bin.39
environment (material)
feces
binning parameters
Reads from ERR7738155 were assembled into contigs (ERZ4560511). The following read sets from this study were the most similar to ERR7738155 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738155,ERR7745876,ERR7738153,ERR7737955,ERR7746794,ERR7745561,ERR7746768,ERR7738236,ERR7745621,ERR7738173. 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 ERZ4560511. 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.
contamination score
0
tRNA extraction software
tRNAscan-SE;2.0.9;-B
reference for biomaterial
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
taxonomic classification
GTDB-TK v1.7.0, r202 database, default parameters
16S recovery software
barrnap;0.9;--kingdom bac
environment (biome)
terrestrial biome
environment (feature)
human-associated habitat
geographic location (country and/or sea)
Tanzania
unique standard tRNAs extracted
18
16S recovered
FALSE
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics.
taxonomic identity marker
multi-marker approach
MAG coverage depth
14.79
completeness score
94.3
geographic location (latitude)
-3.55
most complete 16S rRNA recovered
NA
contamination screening parameters
All reads in ERR7738155 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).
isolation_source
human feces
ENA-FIRST-PUBLIC
2022-04-01
ENA-LAST-UPDATE
2022-04-01