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Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data
Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, bu...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737671/ https://www.ncbi.nlm.nih.gov/pubmed/28498906 http://dx.doi.org/10.1093/dnares/dsx012 |
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author | Kobayashi, Masaaki Ohyanagi, Hajime Takanashi, Hideki Asano, Satomi Kudo, Toru Kajiya-Kanegae, Hiromi Nagano, Atsushi J. Tainaka, Hitoshi Tokunaga, Tsuyoshi Sazuka, Takashi Iwata, Hiroyoshi Tsutsumi, Nobuhiro Yano, Kentaro |
author_facet | Kobayashi, Masaaki Ohyanagi, Hajime Takanashi, Hideki Asano, Satomi Kudo, Toru Kajiya-Kanegae, Hiromi Nagano, Atsushi J. Tainaka, Hitoshi Tokunaga, Tsuyoshi Sazuka, Takashi Iwata, Hiroyoshi Tsutsumi, Nobuhiro Yano, Kentaro |
author_sort | Kobayashi, Masaaki |
collection | PubMed |
description | Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)). |
format | Online Article Text |
id | pubmed-5737671 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57376712018-01-04 Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data Kobayashi, Masaaki Ohyanagi, Hajime Takanashi, Hideki Asano, Satomi Kudo, Toru Kajiya-Kanegae, Hiromi Nagano, Atsushi J. Tainaka, Hitoshi Tokunaga, Tsuyoshi Sazuka, Takashi Iwata, Hiroyoshi Tsutsumi, Nobuhiro Yano, Kentaro DNA Res Full Papers Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)). Oxford University Press 2017-08 2017-05-11 /pmc/articles/PMC5737671/ /pubmed/28498906 http://dx.doi.org/10.1093/dnares/dsx012 Text en © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Full Papers Kobayashi, Masaaki Ohyanagi, Hajime Takanashi, Hideki Asano, Satomi Kudo, Toru Kajiya-Kanegae, Hiromi Nagano, Atsushi J. Tainaka, Hitoshi Tokunaga, Tsuyoshi Sazuka, Takashi Iwata, Hiroyoshi Tsutsumi, Nobuhiro Yano, Kentaro Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title | Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title_full | Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title_fullStr | Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title_full_unstemmed | Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title_short | Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data |
title_sort | heap: a highly sensitive and accurate snp detection tool for low-coverage high-throughput sequencing data |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737671/ https://www.ncbi.nlm.nih.gov/pubmed/28498906 http://dx.doi.org/10.1093/dnares/dsx012 |
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