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

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 ove...

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Autores principales: Pajuste, Fanny-Dhelia, Kaplinski, Lauris, Möls, Märt, Puurand, Tarmo, Lepamets, Maarja, Remm, Maido
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451431/
https://www.ncbi.nlm.nih.gov/pubmed/28566690
http://dx.doi.org/10.1038/s41598-017-02487-5
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author Pajuste, Fanny-Dhelia
Kaplinski, Lauris
Möls, Märt
Puurand, Tarmo
Lepamets, Maarja
Remm, Maido
author_facet Pajuste, Fanny-Dhelia
Kaplinski, Lauris
Möls, Märt
Puurand, Tarmo
Lepamets, Maarja
Remm, Maido
author_sort Pajuste, Fanny-Dhelia
collection PubMed
description 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/).
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spelling pubmed-54514312017-06-02 FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads Pajuste, Fanny-Dhelia Kaplinski, Lauris Möls, Märt Puurand, Tarmo Lepamets, Maarja Remm, Maido Sci Rep Article 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/). Nature Publishing Group UK 2017-05-31 /pmc/articles/PMC5451431/ /pubmed/28566690 http://dx.doi.org/10.1038/s41598-017-02487-5 Text en © The Author(s) 2017 Open Access 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 http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Pajuste, Fanny-Dhelia
Kaplinski, Lauris
Möls, Märt
Puurand, Tarmo
Lepamets, Maarja
Remm, Maido
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
title 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_short 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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451431/
https://www.ncbi.nlm.nih.gov/pubmed/28566690
http://dx.doi.org/10.1038/s41598-017-02487-5
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