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Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"

Alla Mikheenko; Andrey Prjibelski; Vladislav Saveliev; Dmitry Antipov; Alexey Gurevich


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  <identifier identifierType="DOI">10.5281/zenodo.1240963</identifier>
  <creators>
    <creator>
      <creatorName>Alla Mikheenko</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3400-9719</nameIdentifier>
      <affiliation>Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia</affiliation>
    </creator>
    <creator>
      <creatorName>Andrey Prjibelski</creatorName>
      <affiliation>Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia</affiliation>
    </creator>
    <creator>
      <creatorName>Vladislav Saveliev</creatorName>
      <affiliation>Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia</affiliation>
    </creator>
    <creator>
      <creatorName>Dmitry Antipov</creatorName>
      <affiliation>Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia</affiliation>
    </creator>
    <creator>
      <creatorName>Alexey Gurevich</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5855-3519</nameIdentifier>
      <affiliation>Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Genome assemblies for "Versatile genome assembly evaluation with QUAST-LG"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>genome assembly, genome assembly evaluation</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-04-02</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1240963</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsDocumentedBy">http://cab.spbu.ru/software/quast-lg/</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1050295</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>3.0.0</version>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Supplementary data for&amp;nbsp;A. Mikheenko, A. Prjibelski, V. Saveliev, D. Antipov, A. Gurevich.&amp;nbsp;Versatile genome assembly evaluation with QUAST-LG.&amp;nbsp;ISMB 2018 PROCEEDINGS (&lt;em&gt;Bioinformatics &lt;/em&gt;journal)&lt;/p&gt;

&lt;p&gt;Reference genomes of&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;&lt;em&gt;Saccharomyces cerevisiae &lt;/em&gt;(yeast)&amp;nbsp;version&amp;nbsp;R64-1-1&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;Caenorhabditis&amp;nbsp;elegans&amp;nbsp;&lt;/em&gt;(worm)&amp;nbsp;version&amp;nbsp;WBcel235&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;Drosophila&amp;nbsp;melanogaster&amp;nbsp;&lt;/em&gt;(fruit fly) version&amp;nbsp;BDGP6&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;And&lt;em&gt; de novo&lt;/em&gt; genome assemblies of&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;Yeast_PB (&lt;em&gt;S. cerevisiae&lt;/em&gt;, genome size: 12.1 Mb): Canu, FALCON, Flye, MaSuRCA,&amp;nbsp;Miniasm (from Illumina pair-ends&amp;nbsp;and&amp;nbsp;PacBio SMRT)&lt;/li&gt;
	&lt;li&gt;Yeast_NP (&lt;em&gt;S. cerevisiae&lt;/em&gt;, genome size: 12.1 Mb):&amp;nbsp;Canu, Flye, MaSuRCA,&amp;nbsp;Miniasm (from Illumina pair-ends&amp;nbsp;and Oxford Nanopore)&lt;/li&gt;
	&lt;li&gt;Worm_PB (&lt;em&gt;C. elegans&lt;/em&gt;, genome size:&amp;nbsp;100.3 Mb):&amp;nbsp;Canu, FALCON, Flye, MaSuRCA,&amp;nbsp;Miniasm (from Illumina pair-ends&amp;nbsp;and&amp;nbsp;PacBio SMRT)&lt;/li&gt;
	&lt;li&gt;Fly_MP (&lt;em&gt;D. melanogaster&lt;/em&gt;,&amp;nbsp;genome size:&amp;nbsp;137.6 Mb): ABySS2, MaSuRCA,&amp;nbsp;Meraculous, Platanus, SOAPdenovo2, SPAdes (from Illumina pair-ends&amp;nbsp;and&amp;nbsp;mate-pairs)&lt;/li&gt;
	&lt;li&gt;Human_MP (&lt;em&gt;H. sapiens&lt;/em&gt;, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends&amp;nbsp;and&amp;nbsp;mate-pairs)&lt;/li&gt;
	&lt;li&gt;Human_NP (&lt;em&gt;H. sapiens&lt;/em&gt;, genome size: 3.1 Gb): UpperBound assembly only (from Illumina pair-ends&amp;nbsp;and&amp;nbsp;Oxford Nanopore)&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;Each pack (items 1-4) is accompanied with the upper bound&amp;nbsp;assembly created with QUAST-LG (for computing theoretical limits on assembly correctness and completeness for a particular genome and set of reads). For more information, interactive QUAST-LG reports, and links to &lt;em&gt;de novo&lt;/em&gt; assemblies of the human datasets please visit&amp;nbsp;http://cab.spbu.ru/software/quast-lg/ or write to&amp;nbsp;&lt;em&gt;quast.support@cab.spbu.ru.&lt;/em&gt;&lt;/p&gt;</description>
  </descriptions>
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