FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.
Identifieur interne : 000C77 ( PubMed/Curation ); précédent : 000C76; suivant : 000C78FastGT: 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Sequence Analysis, DNA.
- statistics & numerical data : Sequence Analysis, DNA.
- Algorithms, Bayes Theorem, Benchmarking, Genome, Human, Genotype, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, Reproducibility of Results, Software.
Abstract
We have developed a computational method that counts the frequencies of unique k-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 k-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/).
DOI: 10.1038/s41598-017-02487-5
PubMed: 28566690
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000C77
Links to Exploration step
pubmed:28566690Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.</title><author><name sortKey="Pajuste, Fanny Dhelia" sort="Pajuste, Fanny Dhelia" uniqKey="Pajuste F" first="Fanny-Dhelia" last="Pajuste">Fanny-Dhelia Pajuste</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. maido.remm@ut.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28566690</idno><idno type="pmid">28566690</idno><idno type="doi">10.1038/s41598-017-02487-5</idno><idno type="wicri:Area/PubMed/Corpus">000C77</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000C77</idno><idno type="wicri:Area/PubMed/Curation">000C77</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000C77</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.</title><author><name sortKey="Pajuste, Fanny Dhelia" sort="Pajuste, Fanny Dhelia" uniqKey="Pajuste F" first="Fanny-Dhelia" last="Pajuste">Fanny-Dhelia Pajuste</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, 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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. maido.remm@ut.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Bayes Theorem</term><term>Benchmarking</term><term>Genome, Human</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Reproducibility of Results</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Analysis, DNA (statistics & numerical data)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Génome humain</term><term>Génotype</term><term>Humains</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term><term>Reproductibilité des résultats</term><term>Référenciation</term><term>Séquençage nucléotidique à haut débit</term><term>Théorème de Bayes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Bayes Theorem</term><term>Benchmarking</term><term>Genome, Human</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Reproducibility of Results</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Génome humain</term><term>Génotype</term><term>Humains</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term><term>Reproductibilité des résultats</term><term>Référenciation</term><term>Séquençage nucléotidique à haut débit</term><term>Théorème de Bayes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We have developed a computational method that counts the frequencies of unique k-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 k-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/).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28566690</PMID><DateCompleted><Year>2018</Year><Month>12</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>14</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>05</Month><Day>31</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.</ArticleTitle><Pagination><MedlinePgn>2537</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-017-02487-5</ELocationID><Abstract><AbstractText>We have developed a computational method that counts the frequencies of unique k-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 k-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/).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pajuste</LastName><ForeName>Fanny-Dhelia</ForeName><Initials>FD</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaplinski</LastName><ForeName>Lauris</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Möls</LastName><ForeName>Märt</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Puurand</LastName><ForeName>Tarmo</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lepamets</LastName><ForeName>Maarja</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Remm</LastName><ForeName>Maido</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. maido.remm@ut.ee.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>05</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci Rep</MedlineTA><NlmUniqueID>101563288</NlmUniqueID><ISSNLinking>2045-2322</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001499" MajorTopicYN="N">Bayes Theorem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019985" MajorTopicYN="N">Benchmarking</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015894" MajorTopicYN="Y">Genome, Human</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName><QualifierName UI="Q000706" MajorTopicYN="N">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>07</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>6</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>6</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28566690</ArticleId><ArticleId IdType="doi">10.1038/s41598-017-02487-5</ArticleId><ArticleId IdType="pii">10.1038/s41598-017-02487-5</ArticleId><ArticleId IdType="pmc">PMC5451431</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>PeerJ. 2017 May 18;5:e3353</Citation><ArticleIdList><ArticleId IdType="pubmed">28533988</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2012 Mar 04;9(4):357-9</Citation><ArticleIdList><ArticleId IdType="pubmed">22388286</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(1):e30377</Citation><ArticleIdList><ArticleId IdType="pubmed">22276185</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2014;15(11):509</Citation><ArticleIdList><ArticleId IdType="pubmed">25398208</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Aug 15;28(16):2097-105</Citation><ArticleIdList><ArticleId IdType="pubmed">22668792</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2014 Jul 15;30(14):1950-7</Citation><ArticleIdList><ArticleId IdType="pubmed">24618471</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2017 Jan;27(1):157-164</Citation><ArticleIdList><ArticleId IdType="pubmed">27903644</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 May 1;25(9):1105-11</Citation><ArticleIdList><ArticleId IdType="pubmed">19289445</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2014 Oct 15;30(20):2843-51</Citation><ArticleIdList><ArticleId IdType="pubmed">24974202</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2015 Apr 15;31(8):1169-75</Citation><ArticleIdList><ArticleId IdType="pubmed">25504847</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation><ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2012 Oct 12;338(6104):222-6</Citation><ArticleIdList><ArticleId IdType="pubmed">22936568</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2015 Jun 17;10(6):e0130821</Citation><ArticleIdList><ArticleId IdType="pubmed">26083032</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2010 Sep;20(9):1297-303</Citation><ArticleIdList><ArticleId IdType="pubmed">20644199</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 2014 Jan;52(1):139-46</Citation><ArticleIdList><ArticleId IdType="pubmed">24172157</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Aug 15;25(16):2078-9</Citation><ArticleIdList><ArticleId IdType="pubmed">19505943</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Med. 2011 Nov 22;3(11):74</Citation><ArticleIdList><ArticleId IdType="pubmed">22113004</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Med. 2013 Mar 27;5(3):28</Citation><ArticleIdList><ArticleId IdType="pubmed">23537139</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Mar 1;26(5):589-95</Citation><ArticleIdList><ArticleId IdType="pubmed">20080505</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Commun. 2015 Feb 25;6:6275</Citation><ArticleIdList><ArticleId IdType="pubmed">25711446</ArticleId></ArticleIdList></Reference><Reference><Citation>Hum Genomics. 2014 Jul 30;8:14</Citation><ArticleIdList><ArticleId IdType="pubmed">25078893</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2016 Mar 11;17 :125</Citation><ArticleIdList><ArticleId IdType="pubmed">26968756</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Mar 1;29(5):652-3</Citation><ArticleIdList><ArticleId IdType="pubmed">23325618</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2016 Jan 4;44(D1):D7-19</Citation><ArticleIdList><ArticleId IdType="pubmed">26615191</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Biol. 2010 Nov;17(11):1549-60</Citation><ArticleIdList><ArticleId IdType="pubmed">20973743</ArticleId></ArticleIdList></Reference><Reference><Citation>Gigascience. 2015 Dec 03;4:58</Citation><ArticleIdList><ArticleId IdType="pubmed">26640690</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2014 Dec;46(12):1350-5</Citation><ArticleIdList><ArticleId IdType="pubmed">25326702</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2014 Mar;32(3):246-51</Citation><ArticleIdList><ArticleId IdType="pubmed">24531798</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2016 Jun 20;17(1):132</Citation><ArticleIdList><ArticleId IdType="pubmed">27323842</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2015 May 15;31(10):1577-83</Citation><ArticleIdList><ArticleId IdType="pubmed">25609790</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2014 Nov 15;30(22):3264-5</Citation><ArticleIdList><ArticleId IdType="pubmed">25075116</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2015 May 15;31(10):1569-76</Citation><ArticleIdList><ArticleId IdType="pubmed">25609798</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2014 Mar 03;15(3):R46</Citation><ArticleIdList><ArticleId IdType="pubmed">24580807</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 1999 Aug;9(8):677-9</Citation><ArticleIdList><ArticleId IdType="pubmed">10447503</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2013 May 29;14(5):R51</Citation><ArticleIdList><ArticleId IdType="pubmed">23718773</ArticleId></ArticleIdList></Reference><Reference><Citation>Gene. 2014 Aug 1;546(1):25-34</Citation><ArticleIdList><ArticleId IdType="pubmed">24858075</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000C77 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 000C77 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Curation
|type= RBID
|clé= pubmed:28566690
|texte= FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:28566690" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |