High-quality MAG for Candidatus Electrothrix laxa from marine sediment (Hou)

BioSample Accession(s)

SAMEA14373207, ERS11967915

assembly software

metaFlye;2.9;nano-hq

environment (material)

sediment

collection date

2021

sample derived from

ERS11891750,ERS11891751

geographic location (longitude)

not provided

binning parameters

Ensemble binning using coverage and kmer

contamination score

2.55

ENA-FIRST-PUBLIC

2022-10-26

ENA-LAST-UPDATE

2024-01-09

completeness software

checkm

environment (biome)

aquatic biome

environment (feature)

marine

geographic location (country and/or sea)

Denmark

ENA-CHECKLIST

ERC000011

binning software

MetaBAT2, Vamb, MaxBin2, metaBinner, DAS Tool

organism

Candidatus Electrothrix laxa

assembly quality

Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs

taxonomic identity marker

multi-marker approach

completeness score

92

geographic location (latitude)

not provided

scientific_name

Candidatus Electrothrix laxa

investigation type

metagenome-assembled genome

metagenomic source

marine metagenome (Taxon: 408172)

project name

Recovery of cable bacteria and associate genomes

sequencing method

Nanopore,Illumina

isolation_source

Marine sediment

Nanopore R9.4.1 chemistry basecalled with Guppy 5.0.7 in SUP mode

BioSample Accession(s)

SAMEA14300421, ERS11891750

ENA-CHECKLIST

ERC000011

ENA-FIRST-PUBLIC

2022-10-26

organism

metagenome

ENA-LAST-UPDATE

2022-10-26

scientific_name

metagenome

Illumina NovoSeq sequencing reads

BioSample Accession(s)

SAMEA14300422, ERS11891751

ENA-CHECKLIST

ERC000011

ENA-FIRST-PUBLIC

2022-10-26

organism

metagenome

ENA-LAST-UPDATE

2022-10-26

scientific_name

metagenome

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX9218846" alias="webin-reads-HOU-NP-R941" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX9218846</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">webin-reads-HOU-NP-R941</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: HOU-NP-R941</TITLE>
  <STUDY_REF accession="ERP137283">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP137283</PRIMARY_ID>
      <SECONDARY_ID>PRJEB52550</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Nanopore R9.4.1 chemistry basecalled with Guppy 5.0.7 in SUP mode</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS11891750">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS11891750</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA14300421</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-NP-20211206b</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS11891750</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA13291518</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX9218846&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX9218846&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX9219151" alias="webin-reads-HOU-IL" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX9219151</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">webin-reads-HOU-IL</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: HOU-IL</TITLE>
  <STUDY_REF accession="ERP137283">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP137283</PRIMARY_ID>
      <SECONDARY_ID>PRJEB52550</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Illumina NovaSeq sequencing reads</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS11891751">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS11891751</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA14300422</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-IL-20220215</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS11891751</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA13308896</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX9219151&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX9219151&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>