FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
Identifieur interne : 000D85 ( Main/Exploration ); précédent : 000D84; suivant : 000D86FastGT: 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
Url:
DOI: 10.1038/s41598-017-02487-5
PubMed: 28566690
PubMed Central: 5451431
Affiliations:
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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><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"><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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L">L Florea</name></author><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name></author><author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name></author><author><name sortKey="Zimin, A" uniqKey="Zimin A">A Zimin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lim, E C" uniqKey="Lim E">E-C Lim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhao, X" uniqKey="Zhao X">X Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kimura, K" uniqKey="Kimura K">K Kimura</name></author><author><name sortKey="Koike, A" uniqKey="Koike A">A Koike</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, M" uniqKey="Meyer M">M 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sortKey="Chikhi, R" uniqKey="Chikhi R">R Chikhi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roy, Rs" uniqKey="Roy R">RS Roy</name></author><author><name sortKey="Bhattacharya, D" uniqKey="Bhattacharya D">D Bhattacharya</name></author><author><name sortKey="Schliep, A" uniqKey="Schliep A">A Schliep</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roberts, A" uniqKey="Roberts A">A Roberts</name></author><author><name sortKey="Pachter, L" uniqKey="Pachter L">L Pachter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author><author><name sortKey="Pachter, L" uniqKey="Pachter L">L Pachter</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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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