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ahmedmagds/GNUVID: GNUVID v2.3

Ahmed M Moustafa


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  <identifier identifierType="DOI">10.5281/zenodo.5115432</identifier>
  <creators>
    <creator>
      <creatorName>Ahmed M Moustafa</creatorName>
      <affiliation>Children's Hospital of Philadelphia</affiliation>
    </creator>
  </creators>
  <titles>
    <title>ahmedmagds/GNUVID: GNUVID v2.3</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-07-20</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5115432</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/ahmedmagds/GNUVID/tree/v2.3</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3927062</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>v2.3</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;ul&gt;
&lt;li&gt;999,106 High Quality GISAID sequences have been included in this analysis from a total of 2,012,563 sequences.&lt;/li&gt;
&lt;li&gt;GNUVID compressed the 9991060 ORFs in the 999106 genomes to 549768 unique alleles.&lt;/li&gt;
&lt;li&gt;523727 Sequence Types (STs) have been assigned in this dataset and were clustered in 2888 clonal complexes (CCs).&lt;/li&gt;
&lt;li&gt;GNUVID now reports the WHO Naming system for VOCs/VOIs (e.g. Alpha, Beta..etc) as per the WHO updated on 07/06/2021.&lt;/li&gt;
&lt;li&gt;GNUVID now excludes genomes that does not pass quality check for sequence length (20000) and proportion of ambiguity (Ns) (0.3). User can change these cutoffs.&lt;/li&gt;
&lt;li&gt;A table showing summary information of the 177 Active Clonal Complexes (CCs) can be found &lt;a href="https://github.com/ahmedmagds/GNUVID/tree/master/db"&gt;here&lt;/a&gt;. A full report for the 2888 CCs can be found &lt;a href="https://github.com/ahmedmagds/GNUVID/blob/master/db/GNUVID_06212021_CCs_report.txt"&gt;here&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
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