| collection date | 2014-08-14 |
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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 | METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_6_2333.15 |
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| 18S rRNAs recovered | 0 |
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| 18S recovered | FALSE |
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| 18S recovery software | barrnap;0.9;--kingdom euk |
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| 28S rRNAs recovered | 0 |
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| 5.8S rRNAs recovered | 0 |
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| 5S rRNAs recovered | 0 |
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| BUSCO Completeness | 90 |
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| BUSCO lineage | stramenopiles_odb10 |
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| BUSCO string | C:90.0%[S:87.0%,D:3.0%],F:2.0%,M:8.0%,n:100 |
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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 | SAMEA13794522 |
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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 |
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| MAG coverage depth | 13.84 |
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| MAG coverage software | Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) 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__Hadza_MoBio_hadza-E-H_N_6_2333.15 |
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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 ERR7745388 were assembled into contigs (ERZ4559653). The following read sets from this study were the most similar to ERR7745388 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745388,ERR7738181,ERR7738158,ERR7738146,ERR7745412,ERR7738269,ERR7738185,ERR7745403,ERR7745582,ERR7738611. 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 ERZ4559653. 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 |
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| completeness approach | EukCC v2.1.0 based on similarity to taxid: 12967 |
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| completeness score | 95.85 |
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| completeness software | EukCC v2.1.0; BUSCO v5.2.2 |
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| contamination score | 0.46 |
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| contamination screening input | reads |
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| contamination screening parameters | All reads in ERR7745388 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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| metagenomic source | human gut metagenome |
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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 | 199 |
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| reassembly post binning | No |
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| sample derived from | ERS2586203 |
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| sequencing method | Illumina NovaSeq 6000 |
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| tRNA extraction software | tRNAscan-SE;2.0.9;-E |
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| tRep classification | Eukaryota|unk|Bigyra|Opalinata|Blastocystidae|Blastocystis|Blastocystis sp. subtype 4 |
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| tRep species confidence | 65.59167089893347 |
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| taxonomic classification | taxRep v0.5.3 vs UniRef100 (5 Mar 2020) |
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| taxonomic identity marker | multi-marker approach |
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| unique standard tRNAs extracted | 20 |
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