2024-01-01
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA113429185
External Id
ETH ZURICH
INSDC center name
2023-05-14T10:44:56Z
INSDC last update
public
INSDC status
ERS15424303
SRA accession
ANT28_SAMPLE241_METAG_CPHJOAPH
Submitter Id
Multiple fragments (101 scaffolds) with little to no review of assembly other than reporting of standard assembly (N50 of 33.3kbp).
assembly quality
metaSPAdes;v.3.11.1;defaults
assembly software
--minContig 2000 and --maxEdges 500
binning parameters
MetaBAT2;v2.12.1
binning software
2012-03-25
collection date
Average of checkm and anvi'o (marker-gene based)
completeness approach
89,08
completeness score
checkm and anvi'o
completeness software
0,20
contamination score
Average of checkm and anvi'o (marker-gene based)
contamination screening input
draft genome assembly from metagenomic biosample SAMEA5958381
description
ocean biome [ENVO:01000048]
environment (biome)
microbial feature [ENVO:01000007]
environment (feature)
sea water [ENVO:00002149]
environment (material)
Southern Ocean
geographic location (country and/or sea)
20
geographic location (depth)
61,24361
geographic location (latitude)
57,07361
geographic location (longitude)
metagenome
investigation type
ocean water
isolation_source
marine metagenome
metagenomic source
uncultured Planktomarina sp.
organism
Ecogenomics and diversification of the Roseobacter RCA cluster and global biogeography of sublineages
project name
No
reassembly post binning
https://doi.org/10.1038/s41467-022-28128-8
reference for biomaterial
Description of the bioinformatics pipeline in https://doi.org/10.1038/s41586-022-04862-3
relevant standard operating procedures
SAMEA5958381
sample derived from
uncultured Planktomarina sp.
scientific_name
Illumina HiSeq 2500
sequencing method
0.22-3 micrometers
size fraction selected
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina;s__
taxonomic classification
multi-gene approach (GTDBTk:v1.0.2)
taxonomic identity marker
Pseudoplanktomarina bipolaris metagenome-assembled genome
title