FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
Identifieur interne : 000855 ( Pmc/Checkpoint ); précédent : 000854; suivant : 000856FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
Auteurs : Fanny-Dhelia Pajuste [Estonie] ; Lauris Kaplinski [Estonie] ; M Rt Möls [Estonie] ; Tarmo Puurand [Estonie] ; Maarja Lepamets [Estonie] ; Maido Remm [Estonie]Source :
- Scientific Reports [ 2045-2322 ] ; 2017.
Abstract
We have developed a computational method that counts the frequencies of unique
Url:
DOI: 10.1038/s41598-017-02487-5
PubMed: 28566690
PubMed Central: 5451431
Affiliations:
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xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Mathematics and Statistics,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Puurand, Tarmo" sort="Puurand, Tarmo" uniqKey="Puurand T" first="Tarmo" last="Puurand">Tarmo Puurand</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We have developed a computational method that counts the frequencies of unique <italic>k</italic>-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina “Platinum” genomes is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides <italic>k</italic>-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including >23,000 SNVs from Y chromosome. The source code of FastGT software is available at GitHub (https://github.com/bioinfo-ut/GenomeTester4/).</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckenna, A" uniqKey="Mckenna A">A McKenna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Highnam, G" uniqKey="Highnam G">G Highnam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zook, Jm" uniqKey="Zook J">JM Zook</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="O Awe, J" uniqKey="O Awe J">J O’Rawe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pirooznia, M" uniqKey="Pirooznia M">M Pirooznia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lee, H" uniqKey="Lee H">H Lee</name></author><author><name sortKey="Schatz, Mc" uniqKey="Schatz M">MC Schatz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weisenfeld, Ni" uniqKey="Weisenfeld N">NI Weisenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wen, J" uniqKey="Wen J">J Wen</name></author><author><name sortKey="Chan, Rhf" uniqKey="Chan R">RHF Chan</name></author><author><name sortKey="Yau, S C" uniqKey="Yau S">S-C 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group UK</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28566690</article-id><article-id pub-id-type="pmc">5451431</article-id><article-id pub-id-type="publisher-id">2487</article-id><article-id pub-id-type="doi">10.1038/s41598-017-02487-5</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Pajuste</surname><given-names>Fanny-Dhelia</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Kaplinski</surname><given-names>Lauris</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Möls</surname><given-names>Märt</given-names></name><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Puurand</surname><given-names>Tarmo</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Lepamets</surname><given-names>Maarja</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Remm</surname><given-names>Maido</given-names></name><address><email>maido.remm@ut.ee</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Mathematics and Statistics,</institution><institution>University of Tartu,</institution></institution-wrap>Tartu, Estonia</aff></contrib-group><pub-date pub-type="epub"><day>31</day><month>5</month><year>2017</year></pub-date><pub-date pub-type="pmc-release"><day>31</day><month>5</month><year>2017</year></pub-date><pub-date pub-type="collection"><year>2017</year></pub-date><volume>7</volume><elocation-id>2537</elocation-id><history><date date-type="received"><day>21</day><month>7</month><year>2016</year></date><date date-type="accepted"><day>12</day><month>4</month><year>2017</year></date></history><permissions><copyright-statement>© The Author(s) 2017</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold> This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>.</license-p></license></permissions><abstract id="Abs1"><p>We have developed a computational method that counts the frequencies of unique <italic>k</italic>-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina “Platinum” genomes is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides <italic>k</italic>-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including >23,000 SNVs from Y chromosome. The source code of FastGT software is available at GitHub (https://github.com/bioinfo-ut/GenomeTester4/).</p></abstract><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2017</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>Estonie</li></country></list><tree><country name="Estonie"><noRegion><name sortKey="Pajuste, Fanny Dhelia" sort="Pajuste, Fanny Dhelia" uniqKey="Pajuste F" first="Fanny-Dhelia" last="Pajuste">Fanny-Dhelia Pajuste</name></noRegion><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><name sortKey="Puurand, Tarmo" sort="Puurand, Tarmo" uniqKey="Puurand T" first="Tarmo" last="Puurand">Tarmo Puurand</name><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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