ERR7738937_bin.56
uncultured Thomasclavelia sp.
This sample represents an uncultured Erysipelatoclostridium sp. MAG assembled and binned from ERR7738937.
collection_date
2017
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
SRS9383899
contamination screening input
reads
geographic location (longitude)
-122.1697
geographic location (elevation)
29
number of standard tRNAs extracted
39
CheckM strain heterogeneity
0
ENA-FIRST-PUBLIC
2022-04-01T08:27:36Z
ENA-LAST-UPDATE
2022-04-01T08:27:36Z
completeness software
CheckM;1.1.2;lineage_wf
nucleic acid extraction
https://doi.org/10.1016/j.cell.2021.06.019
completeness approach
CheckM marker lineage: k__Bacteria (UID2372)
GTDB r202 classification
d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Erysipelatoclostridium;s__Erysipelatoclostridium spiroforme
binning software
MetaBAT2 v2.15; MAGpurify v2.1.0
inter-study species representative
GUT_GENOME103849
5S rRNAs recovered
0
organism
uncultured Erysipelatoclostridium sp.
sample collection device or method
https://doi.org/10.1016/j.cell.2021.06.019
scientific_name
uncultured Erysipelatoclostridium sp.
investigation type
metagenome-assembled genome
MAG coverage software
Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) 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 Californian gut microbiome
sequencing method
Illumina NovaSeq 6000
most complete 23S rRNA recovered
NA
23S rRNAs recovered
0
most complete 5S rRNA recovered
NA
reassembly post binning
No
16S rRNAs recovered
0
intra-study species representative
ERR7738937_bin.56
environment (material)
feces
binning parameters
Reads from ERR7738937 were assembled into contigs (ERZ4558872). The following read sets from this study were the most similar to ERR7738937 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738937,ERR7738276. 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 ERZ4558872. 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.
contamination score
0
tRNA extraction software
tRNAscan-SE;2.0.9;-B
reference for biomaterial
https://doi.org/10.1016/j.cell.2021.06.019
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)
USA
unique standard tRNAs extracted
20
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
16.91
completeness score
98.11
geographic location (latitude)
37.4275
most complete 16S rRNA recovered
NA
contamination screening parameters
All reads in ERR7738937 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