FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
Identifieur interne : 001A56 ( Ncbi/Curation ); précédent : 001A55; suivant : 001A57FastGT: 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
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PMC:5451431Le document en format XML
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<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>
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<term>Analyse de séquence d'ADN ()</term>
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<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>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Bayes Theorem</term>
<term>Benchmarking</term>
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<term>Genotype</term>
<term>High-Throughput Nucleotide Sequencing</term>
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<term>Polymorphisme de nucléotide simple</term>
<term>Reproductibilité des résultats</term>
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<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>
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<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
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