FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

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...

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Autores principales:	Fanny-Dhelia Pajuste, Lauris Kaplinski, Märt Möls, Tarmo Puurand, Maarja Lepamets, Maido Remm
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e60e1692858c4df3bb8f5736e3177bde
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spelling	oai:doaj.org-article:e60e1692858c4df3bb8f5736e3177bde2021-12-02T12:32:14ZFastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads10.1038/s41598-017-02487-52045-2322https://doaj.org/article/e60e1692858c4df3bb8f5736e3177bde2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02487-5https://doaj.org/toc/2045-2322Abstract 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/).Fanny-Dhelia PajusteLauris KaplinskiMärt MölsTarmo PuurandMaarja LepametsMaido RemmNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Fanny-Dhelia Pajuste Lauris Kaplinski Märt Möls Tarmo Puurand Maarja Lepamets Maido Remm FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
description	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/).
format	article
author	Fanny-Dhelia Pajuste Lauris Kaplinski Märt Möls Tarmo Puurand Maarja Lepamets Maido Remm
author_facet	Fanny-Dhelia Pajuste Lauris Kaplinski Märt Möls Tarmo Puurand Maarja Lepamets Maido Remm
author_sort	Fanny-Dhelia Pajuste
title	FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title_short	FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title_full	FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title_fullStr	FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title_full_unstemmed	FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title_sort	fastgt: an alignment-free method for calling common snvs directly from raw sequencing reads
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/e60e1692858c4df3bb8f5736e3177bde
work_keys_str_mv	AT fannydheliapajuste fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT lauriskaplinski fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT martmols fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT tarmopuurand fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT maarjalepamets fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT maidoremm fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads
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FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

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