Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We devel...

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Autores principales:	Shunichi Kosugi, Satoshi Natsume, Kentaro Yoshida, Daniel MacLean, Liliana Cano, Sophien Kamoun, Ryohei Terauchi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/073e8266e16a424cbe5a7e604d0da610
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spelling	oai:doaj.org-article:073e8266e16a424cbe5a7e604d0da6102021-11-18T08:51:57ZCoval: improving alignment quality and variant calling accuracy for next-generation sequencing data.1932-620310.1371/journal.pone.0075402https://doaj.org/article/073e8266e16a424cbe5a7e604d0da6102013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24116042/?tool=EBIhttps://doaj.org/toc/1932-6203Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.Shunichi KosugiSatoshi NatsumeKentaro YoshidaDaniel MacLeanLiliana CanoSophien KamounRyohei TerauchiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e75402 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shunichi Kosugi Satoshi Natsume Kentaro Yoshida Daniel MacLean Liliana Cano Sophien Kamoun Ryohei Terauchi Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
description	Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.
format	article
author	Shunichi Kosugi Satoshi Natsume Kentaro Yoshida Daniel MacLean Liliana Cano Sophien Kamoun Ryohei Terauchi
author_facet	Shunichi Kosugi Satoshi Natsume Kentaro Yoshida Daniel MacLean Liliana Cano Sophien Kamoun Ryohei Terauchi
author_sort	Shunichi Kosugi
title	Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
title_short	Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
title_full	Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
title_fullStr	Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
title_full_unstemmed	Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
title_sort	coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/073e8266e16a424cbe5a7e604d0da610
work_keys_str_mv	AT shunichikosugi covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT satoshinatsume covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT kentaroyoshida covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT danielmaclean covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT lilianacano covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT sophienkamoun covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata AT ryoheiterauchi covalimprovingalignmentqualityandvariantcallingaccuracyfornextgenerationsequencingdata
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Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

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