barrnap (version 0.9)
16S recovery software
No
16s recovered
no
23s recovered
no
5s recovered
2024-03-27
ENA first public
ERC000047
ENA-CHECKLIST
48.9
%
GC content
CAU
INSDC center name
public
INSDC status
Bowtie (version 2.2.5) with jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1)
MAG coverage software
ERS18592641
SRA accession
ena-SAMPLE-TAB-22-03-2024-10:43:23:864-115604
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes hybrid (SPAdes version 3.13.1)
assembly software
coverage depth and k-mer binning. Scaffolds were filtered for min. length 1000bp and min. coverage 7.7815. Quality-controlled metagenomic reads were mapped back to the filtered scaffolds with Bowtie (version 2.2.5); the insert size was 0–1000 bp in very sensitive, non-deterministic, “fr” stranded mode with end-to-end alignment. Non-unique mappings and unaligned reads were discarded. The scaffold coverage depth was determined with the jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1). Scaffolds were broken into 10 kbp chunks for CONCOCT.
binning parameters
MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), MaxBin (version 2.2.4), DASTool (version 1.1.2)
binning software
host associated gut microbiome
broad-scale environmental context
2017-02-14
collection date
96.4
%
completeness score
CheckM (version 1.1.2)
completeness software
0.8
%
contamination score
MAG_BA_Duncaniella_freteri_01: Metagenomic assembled genome (MAG) from colon contents of n=52, untreated, wild-type, male C57BL/6J/Ukj mice, aged 2-30 months. Full cohort assembly of all metagenomic samples assembled together from short and long read sequencing with metaSpades hybrid. Coverage and k-mer binning with MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), and MaxBin (version 2.2.4) produced 252 bins which were refined into 181, high to medium quality MAGs via DASTool.
description
host associated gut microbiome
environmental medium
Germany
geographic location (country and/or sea)
50.9
DD
geographic location (latitude)
11.6
DD
geographic location (longitude)
mouse colon contents
isolation_source
host associated gut microbiome
local environmental context
mouse gut metagenome
metagenomic source
20
number of standard tRNAs extracted
Duncaniella freteri
organism
Baseline aging (BA); Aging-associated loss of metabolic host-microbiome-interactions in mice
project name
ERS18444878,ERS18444879,ERS18444880,ERS18444881,ERS18444882,ERS18444883,ERS18444884,ERS18444885,ERS18444886,ERS18444887,ERS18444888,ERS18444889,ERS18444890,ERS18444891,ERS18444892,ERS18444893,ERS18444894,ERS18444895,ERS18444896,ERS18444897,ERS18444898,ERS18444899,ERS18444900,ERS18444901,ERS18444902,ERS18444903,ERS18444904,ERS18444905,ERS18444906,ERS18444907,ERS18444908,ERS18444909,ERS18444910,ERS18444911,ERS18444912,ERS18444913,ERS18444914,ERS18444915,ERS18444916,ERS18444917,ERS18444918,ERS18444919,ERS18444920,ERS18444921,ERS18444922,ERS18444923,ERS18444924,ERS18444925,ERS18444926,ERS18444927,ERS18444928,ERS18444929,ERS18590020,ERS18590021,ERS18590022,ERS18590023,ERS18590024,ERS18590025,ERS18590026,ERS18590027
sample derived from
Duncaniella freteri
scientific_name
tRNAscan-SE (version 2.0.9)
tRNA extraction software
GTDB-Tk, r214
taxonomic classification
multi-marker approach
taxonomic identity marker
BA_Duncaniella_freteri_01
title