MersV1, PubMed, Corpus, bibRecord, 000455

Haplotype-aware graph indexes.

Identifieur interne : 000455 ( PubMed/Corpus ); précédent : 000454; suivant : 000456

Haplotype-aware graph indexes.

Auteurs : Jouni Sirén ; Erik Garrison ; Adam M. Novak ; Benedict Paten ; Richard Durbin

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.

RBID : pubmed:31406990

Abstract

The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.

DOI: 10.1093/bioinformatics/btz575
PubMed: 31406990

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pubmed:31406990

Le document en format XML

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<author><name sortKey="Siren, Jouni" sort="Siren, Jouni" uniqKey="Siren J" first="Jouni" last="Sirén">Jouni Sirén</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Garrison, Erik" sort="Garrison, Erik" uniqKey="Garrison E" first="Erik" last="Garrison">Erik Garrison</name>
<affiliation><nlm:affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Novak, Adam M" sort="Novak, Adam M" uniqKey="Novak A" first="Adam M" last="Novak">Adam M. Novak</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Paten, Benedict" sort="Paten, Benedict" uniqKey="Paten B" first="Benedict" last="Paten">Benedict Paten</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Durbin, Richard" sort="Durbin, Richard" uniqKey="Durbin R" first="Richard" last="Durbin">Richard Durbin</name>
<affiliation><nlm:affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</nlm:affiliation>
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<author><name sortKey="Siren, Jouni" sort="Siren, Jouni" uniqKey="Siren J" first="Jouni" last="Sirén">Jouni Sirén</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
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<author><name sortKey="Garrison, Erik" sort="Garrison, Erik" uniqKey="Garrison E" first="Erik" last="Garrison">Erik Garrison</name>
<affiliation><nlm:affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Novak, Adam M" sort="Novak, Adam M" uniqKey="Novak A" first="Adam M" last="Novak">Adam M. Novak</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Paten, Benedict" sort="Paten, Benedict" uniqKey="Paten B" first="Benedict" last="Paten">Benedict Paten</name>
<affiliation><nlm:affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Durbin, Richard" sort="Durbin, Richard" uniqKey="Durbin R" first="Richard" last="Durbin">Richard Durbin</name>
<affiliation><nlm:affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</nlm:affiliation>
</affiliation>
</author>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2020" type="published">2020</date>
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<front><div type="abstract" xml:lang="en">The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">31406990</PMID>
<DateRevised><Year>2020</Year>
<Month>03</Month>
<Day>16</Day>
</DateRevised>
<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>36</Volume>
<Issue>2</Issue>
<PubDate><Year>2020</Year>
<Month>Jan</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>Haplotype-aware graph indexes.</ArticleTitle>
<Pagination><MedlinePgn>400-407</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz575</ELocationID>
<Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.</AbstractText>
<AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2.</AbstractText>
<AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText>
<CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sirén</LastName>
<ForeName>Jouni</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Garrison</LastName>
<ForeName>Erik</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Novak</LastName>
<ForeName>Adam M</ForeName>
<Initials>AM</Initials>
<AffiliationInfo><Affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Paten</LastName>
<ForeName>Benedict</ForeName>
<Initials>B</Initials>
<AffiliationInfo><Affiliation>UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Durbin</LastName>
<ForeName>Richard</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>207492/Z/17/Z</GrantID>
<Acronym>WT_</Acronym>
<Agency>Wellcome Trust</Agency>
<Country>United Kingdom</Country>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Bioinformatics</MedlineTA>
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<ISSNLinking>1367-4803</ISSNLinking>
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<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year>
<Month>02</Month>
<Day>20</Day>
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<PubMedPubDate PubStatus="revised"><Year>2019</Year>
<Month>05</Month>
<Day>29</Day>
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<PubMedPubDate PubStatus="accepted"><Year>2019</Year>
<Month>07</Month>
<Day>18</Day>
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Haplotype-aware graph indexes.

Haplotype-aware graph indexes.

Source :

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki