Cargando…
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...
Autores principales: | , , , , , |
---|---|
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 |
_version_ | 1783240173184614400 |
---|---|
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/). |
format | Online Article Text |
id | pubmed-5451431 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT pajustefannydhelia fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT kaplinskilauris fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT molsmart fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT puurandtarmo fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT lepametsmaarja fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads AT remmmaido fastgtanalignmentfreemethodforcallingcommonsnvsdirectlyfromrawsequencingreads |