collection date | 2014-01-26 |
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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 | Tanzania |
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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 Hadza gut microbiome |
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reference for biomaterial | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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sample collection device or method | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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sample name | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_L_11_1531.18 |
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16S rRNAs recovered | 0 |
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16S recovered | FALSE |
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16S recovery software | barrnap;0.9;--kingdom bac |
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23S rRNAs recovered | 0 |
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5S rRNAs recovered | 1 |
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CheckM strain heterogeneity | 0 |
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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 | SAMEA13474892 |
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GTDB r202 classification | d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;s__F23-B02 sp004556755 |
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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 | 2022-04-01T08:22:12Z |
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INSDC last update | 2022-04-01T08:22:12Z |
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INSDC status | public |
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MAG coverage depth | 29.25 |
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MAG coverage software | Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) 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 | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_L_11_1531.18 |
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assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics. |
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assembly software | metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz |
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binning parameters | Reads from ERR7745398 were assembled into contigs (ERZ4560823). The following read sets from this study were the most similar to ERR7745398 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745398,ERR7745431,ERR7745854,ERR7738227,ERR7745625,ERR7738534,ERR7738957,ERR7747128,ERR7738186,ERR7746345. 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 ERZ4560823. 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. |
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binning software | MetaBAT2 v2.15; MAGpurify v2.1.0 |
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completeness approach | CheckM marker lineage: o__Clostridiales (UID1212) |
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completeness score | 90.27 |
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completeness software | CheckM;1.1.2;lineage_wf |
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contamination score | 0 |
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contamination screening input | reads |
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contamination screening parameters | All reads in ERR7745398 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) | 1287 |
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geographic location (latitude) | -3.55 |
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geographic location (longitude) | -34.58 |
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inter-study species representative | ERR7745398_bin.18 |
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intra-study species representative | ERR7745854_bin.314 |
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metagenomic source | human gut metagenome |
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most complete 5S rRNA recovered | 0.9243697478991597 |
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nucleic acid extraction | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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number of standard tRNAs extracted | 43 |
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reassembly post binning | No |
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sample derived from | ERS2585786 |
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sequencing method | Illumina NovaSeq 6000 |
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tRNA extraction software | tRNAscan-SE;2.0.9;-B |
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taxonomic classification | GTDB-TK v1.7.0, r202 database, default parameters |
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taxonomic identity marker | multi-marker approach |
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unique standard tRNAs extracted | 20 |
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