Circular MAG for Candidatus Electronema halotolerans from brackish water sediment (Logten)

BioSample Accession(s)

SAMEA14373291, ERS11967999

assembly software

metaFlye;2.9;nano-hq

environment (material)

sediment

collection date

2021

sample derived from

ERS11891752,ERS11891753

geographic location (longitude)

not provided

binning parameters

Ensemble binning using coverage and kmer

contamination score

3.27

ENA-FIRST-PUBLIC

2022-10-26

ENA-LAST-UPDATE

2024-01-09

completeness software

checkm

environment (biome)

aquatic biome

environment (feature)

brackish

geographic location (country and/or sea)

Denmark

ENA-CHECKLIST

ERC000011

binning software

MetaBAT2, Vamb, MaxBin2, metaBinner, DAS Tool

organism

Candidatus Electronema halotolerans

assembly quality

Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better

taxonomic identity marker

multi-marker approach

completeness score

94.05

geographic location (latitude)

not provided

scientific_name

Candidatus Electronema halotolerans

investigation type

metagenome-assembled genome

metagenomic source

sediment metagenome (Taxon: 749907)

project name

Recovery of cable bacteria and associate genomes

sequencing method

Nanopore,Illumina

isolation_source

Brackish water sediment

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

BioSample Accession(s)

SAMEA14300423, ERS11891752

ENA-CHECKLIST

ERC000011

organism

sediment metagenome

collection date

not provided

scientific_name

sediment metagenome

geographic location (country and/or sea)

not provided

Illumina NovoSeq sequencing reads

BioSample Accession(s)

SAMEA14300424, ERS11891753

ENA-CHECKLIST

ERC000011

organism

sediment metagenome

collection date

not provided

scientific_name

sediment metagenome

geographic location (country and/or sea)

not provided

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX9218870" alias="webin-reads-LOGT-NP-R941" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX9218870</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">webin-reads-LOGT-NP-R941</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: LOGT-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="ERS11891752">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS11891752</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA14300423</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-NP-20211206a</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>ERS11891752</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA13296842</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=ERX9218870&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=ERX9218870&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="ERX9219365" alias="webin-reads-LOGT-IL" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX9219365</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">webin-reads-LOGT-IL</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: LOGT-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="ERS11891753">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS11891753</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA14300424</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>ERS11891753</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA13322122</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=ERX9219365&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=ERX9219365&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>