Software Open Access

ahmedmagds/GNUVID: GNUVID v1.3: Globally circulating clonal complexes as of 2020-07-17

Ahmed M Moustafa


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.3966904</identifier>
  <creators>
    <creator>
      <creatorName>Ahmed M Moustafa</creatorName>
      <affiliation>Children's Hospital of Philadelphia</affiliation>
    </creator>
  </creators>
  <titles>
    <title>ahmedmagds/GNUVID: GNUVID v1.3: Globally circulating clonal complexes as of 2020-07-17</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-07-30</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3966904</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/ahmedmagds/GNUVID/tree/v1.3</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>v1.3</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">Summary
&lt;ul&gt;
&lt;li&gt;&lt;p&gt;25594 GISAID sequences have been included in this analysis.&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;GNUVID compressed the 255940 ORFs in the 25594 genomes to 15025 unique alleles.&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;13688 Sequence Types (STs) have been assigned in this dataset and were clustered in 59 clonal complexes (CCs).&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;14 new CCs have been assigned.&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;42 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-07-17).&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;12 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-07-17).&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;5 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-07-17).&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;CC70, CC26, CC343, CC927 and CC1434 have now been called CC550, CC750, CC9999, CC1179 and CC2175 respectively.&lt;/p&gt;
&lt;/li&gt;
&lt;li&gt;&lt;p&gt;Starting from the DB update (07/17/2020), &lt;strong&gt;the nine defining SNPs (C241,C3037,A23403,C8782,G11083,G25563,G26144,T28144,G28882)&lt;/strong&gt; for the six GISAID clades are reported for each CC for easier correlation between the two systems.&lt;/p&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
390
18
views
downloads
All versions This version
Views 390161
Downloads 184
Data volume 563.6 MB183.8 MB
Unique views 334151
Unique downloads 164

Share

Cite as