ERR7738560_bin.90
uncultured Blastocystis sp.
This sample represents an uncultured Blastocystis sp. MAG assembled and binned from ERR7738560.
18S rRNAs recovered
0
18S recovered
FALSE
18S recovery software
barrnap;0.9;--kingdom euk
28S rRNAs recovered
0
5.8S rRNAs recovered
0
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
ENA last update
2022-04-01
External Id
SAMEA13794536
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:28:16Z
INSDC last update
2022-04-01T08:28:16Z
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.
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.
binning software
MetaBAT2 v2.15
collection date
2016
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).
environment (biome)
terrestrial biome
environment (feature)
human-associated habitat
environment (material)
feces
geographic location (country and/or sea)
Nepal
geographic location (elevation)
1400
geographic location (latitude)
28.17
geographic location (longitude)
84.25
investigation type
metagenome-assembled genome
isolation source
human feces
metagenomic source
human gut metagenome
nucleic acid extraction
https://doi.org/10.1371/journal.pbio.2005396
number of standard tRNAs extracted
109
project name
Metagenome sequencing of Nepali gut microbiome
reassembly post binning
No
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 derived from
ERS2787413
sample name
METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ.90
sequencing method
Illumina NovaSeq 6000
tRNA extraction software
tRNAscan-SE;2.0.9;-E
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
unique standard tRNAs extracted
20