| collection date | 2016 |
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| broad-scale environmental context | terrestrial biome |
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| local-scale environmental context | human-associated habitat |
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| environmental medium | feces |
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| geographic location | Nepal |
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| investigation type | metagenome-assembled genome |
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| isolation source | human feces |
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| project name | Metagenome sequencing of Nepali gut microbiome |
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| reference for biomaterial | https://doi.org/10.1371/journal.pbio.2005396 |
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| sample collection device or method | https://doi.org/10.1371/journal.pbio.2005396 |
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| sample name | METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ.90 |
|---|
| 18S rRNAs recovered | 0 |
|---|
| 18S recovered | FALSE |
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| 18S recovery software | barrnap;0.9;--kingdom euk |
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| 28S rRNAs recovered | 0 |
|---|
| 5.8S rRNAs recovered | 0 |
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| 5S rRNAs recovered | 0 |
|---|
| BUSCO Completeness | 76 |
|---|
| BUSCO lineage | stramenopiles_odb10 |
|---|
| BUSCO string | C:76.0%[S:76.0%,D:0.0%],F:6.0%,M:18.0%,n:100 |
|---|
| ENA first public | 2022-04-01 |
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| ENA last update | 2022-04-01 |
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| ENA-CHECKLIST | ERC000011 |
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| External Id | SAMEA13794536 |
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| INSDC center alias | Stanford University School of Medicine |
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| INSDC center name | stanford university school of medicine |
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| INSDC first public | 2022-04-01T08:28:16Z |
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| INSDC last update | 2022-04-01T08:28:16Z |
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| INSDC status | public |
|---|
| MAG coverage depth | 6.78 |
|---|
| MAG coverage software | Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. |
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| Submitter Id | METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ.90 |
|---|
| 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 ERR7738560 were assembled into contigs (ERZ4567601). The following read sets from this study were the most similar to ERR7738560 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738560,ERR7738572,ERR7745908,ERR7745755,ERR7738938,ERR7738451,ERR7738529,ERR7738621,ERR7745346,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 ERZ4567601. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. |
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| binning software | MetaBAT2 v2.15 |
|---|
| completeness approach | EukCC v2.1.0 based on similarity to taxid: 12967 |
|---|
| completeness score | 80.65 |
|---|
| completeness software | EukCC v2.1.0; BUSCO v5.2.2 |
|---|
| contamination score | 0 |
|---|
| contamination screening input | reads |
|---|
| contamination screening parameters | All reads in ERR7738560 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2). |
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| geographic location (elevation) | 1400 |
|---|
| geographic location (latitude) | 28.17 |
|---|
| geographic location (longitude) | 84.25 |
|---|
| metagenomic source | human gut metagenome |
|---|
| nucleic acid extraction | https://doi.org/10.1371/journal.pbio.2005396 |
|---|
| number of standard tRNAs extracted | 109 |
|---|
| reassembly post binning | No |
|---|
| sample derived from | ERS2787413 |
|---|
| sequencing method | Illumina NovaSeq 6000 |
|---|
| tRNA extraction software | tRNAscan-SE;2.0.9;-E |
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| tRep classification | Eukaryota|unk|Bigyra|Opalinata|Blastocystidae|Blastocystis|Blastocystis sp. subtype 1 |
|---|
| tRep species confidence | 95.06700330161196 |
|---|
| taxonomic classification | taxRep v0.5.3 vs UniRef100 (5 Mar 2020) |
|---|
| taxonomic identity marker | multi-marker approach |
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| unique standard tRNAs extracted | 20 |
|---|