| collection date | 2016 |
|---|
| broad-scale environmental context | terrestrial biome |
|---|
| local-scale environmental context | human-associated habitat |
|---|
| environmental medium | feces |
|---|
| geographic location | Nepal |
|---|
| investigation type | metagenome-assembled genome |
|---|
| isolation source | human feces |
|---|
| project name | Metagenome sequencing of Nepali gut microbiome |
|---|
| reference for biomaterial | https://doi.org/10.1371/journal.pbio.2005396 |
|---|
| sample collection device or method | https://doi.org/10.1371/journal.pbio.2005396 |
|---|
| sample name | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ.106 |
|---|
| 16S rRNAs recovered | 0 |
|---|
| 16S recovered | FALSE |
|---|
| 16S recovery software | barrnap;0.9;--kingdom bac |
|---|
| 23S rRNAs recovered | 0 |
|---|
| 5S rRNAs recovered | 1 |
|---|
| CheckM strain heterogeneity | 0 |
|---|
| ENA first public | 2022-04-01 |
|---|
| ENA last update | 2022-04-01 |
|---|
| ENA-CHECKLIST | ERC000011 |
|---|
| External Id | SAMEA13492474 |
|---|
| GTDB r202 classification | d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789;s__UBA3789 sp900543055 |
|---|
| INSDC center alias | Stanford University School of Medicine |
|---|
| INSDC center name | stanford university school of medicine |
|---|
| INSDC first public | 2022-04-01T08:25:45Z |
|---|
| INSDC last update | 2022-04-01T08:25:45Z |
|---|
| INSDC status | public |
|---|
| MAG coverage depth | 16 |
|---|
| MAG coverage software | Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. |
|---|
| Submitter Id | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ.106 |
|---|
| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics. |
|---|
| assembly software | metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz |
|---|
| binning parameters | Reads from ERR7745836 were assembled into contigs (ERZ4567121). The following read sets from this study were the most similar to ERR7745836 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745836,ERR7738229,ERR7745831,ERR7745877,ERR7738545,ERR7738353,ERR7745779,ERR7738558,ERR7738533,ERR7738580. 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 ERZ4567121. 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. |
|---|
| binning software | MetaBAT2 v2.15; MAGpurify v2.1.0 |
|---|
| completeness approach | CheckM marker lineage: k__Bacteria (UID2329) |
|---|
| completeness score | 92.13 |
|---|
| completeness software | CheckM;1.1.2;lineage_wf |
|---|
| contamination score | 0.16 |
|---|
| contamination screening input | reads |
|---|
| contamination screening parameters | All reads in ERR7745836 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2). |
|---|
| geographic location (elevation) | 1400 |
|---|
| geographic location (latitude) | 28.17 |
|---|
| geographic location (longitude) | 84.25 |
|---|
| inter-study species representative | GUT_GENOME108563 |
|---|
| intra-study species representative | ERR7745836_bin.106 |
|---|
| metagenomic source | human gut metagenome |
|---|
| most complete 5S rRNA recovered | 0.6218487394957983 |
|---|
| nucleic acid extraction | https://doi.org/10.1371/journal.pbio.2005396 |
|---|
| number of standard tRNAs extracted | 34 |
|---|
| reassembly post binning | No |
|---|
| sample derived from | ERS2787340 |
|---|
| sequencing method | Illumina NovaSeq 6000 |
|---|
| tRNA extraction software | tRNAscan-SE;2.0.9;-B |
|---|
| taxonomic classification | GTDB-TK v1.7.0, r202 database, default parameters |
|---|
| taxonomic identity marker | multi-marker approach |
|---|
| unique standard tRNAs extracted | 20 |
|---|