Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus

Abstract Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed next-generation sequencing platform with a relatively high insertion and deletion (indel) error rate. A full systematic assessment of the effectiveness of various error correction algorithms i...

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Autores principales:	Liting Song, Wenxun Huang, Juan Kang, Yuan Huang, Hong Ren, Keyue Ding
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3ea364f13c72441ca774d4bcc1642163
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spelling	oai:doaj.org-article:3ea364f13c72441ca774d4bcc16421632021-12-02T12:32:49ZComparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus10.1038/s41598-017-08139-y2045-2322https://doaj.org/article/3ea364f13c72441ca774d4bcc16421632017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08139-yhttps://doaj.org/toc/2045-2322Abstract Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed next-generation sequencing platform with a relatively high insertion and deletion (indel) error rate. A full systematic assessment of the effectiveness of various error correction algorithms in PGM viral datasets (e.g., hepatitis B virus (HBV)) has not been performed. We examined 19 quality-trimmed PGM datasets for the HBV reverse transcriptase (RT) region and found a total error rate of 0.48% ± 0.12%. Deletion errors were clearly present at the ends of homopolymer runs. Tests using both real and simulated data showed that the algorithms differed in their abilities to detect and correct errors and that the error rate and sequencing depth significantly affected the performance. Of the algorithms tested, Pollux showed a better overall performance but tended to over-correct ‘genuine’ substitution variants, whereas Fiona proved to be better at distinguishing these variants from sequencing errors. We found that the combined use of Pollux and Fiona gave the best results when error-correcting Ion Torrent PGM viral data.Liting SongWenxun HuangJuan KangYuan HuangHong RenKeyue DingNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Liting Song Wenxun Huang Juan Kang Yuan Huang Hong Ren Keyue Ding Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
description	Abstract Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed next-generation sequencing platform with a relatively high insertion and deletion (indel) error rate. A full systematic assessment of the effectiveness of various error correction algorithms in PGM viral datasets (e.g., hepatitis B virus (HBV)) has not been performed. We examined 19 quality-trimmed PGM datasets for the HBV reverse transcriptase (RT) region and found a total error rate of 0.48% ± 0.12%. Deletion errors were clearly present at the ends of homopolymer runs. Tests using both real and simulated data showed that the algorithms differed in their abilities to detect and correct errors and that the error rate and sequencing depth significantly affected the performance. Of the algorithms tested, Pollux showed a better overall performance but tended to over-correct ‘genuine’ substitution variants, whereas Fiona proved to be better at distinguishing these variants from sequencing errors. We found that the combined use of Pollux and Fiona gave the best results when error-correcting Ion Torrent PGM viral data.
format	article
author	Liting Song Wenxun Huang Juan Kang Yuan Huang Hong Ren Keyue Ding
author_facet	Liting Song Wenxun Huang Juan Kang Yuan Huang Hong Ren Keyue Ding
author_sort	Liting Song
title	Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
title_short	Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
title_full	Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
title_fullStr	Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
title_full_unstemmed	Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus
title_sort	comparison of error correction algorithms for ion torrent pgm data: application to hepatitis b virus
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/3ea364f13c72441ca774d4bcc1642163
work_keys_str_mv	AT litingsong comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus AT wenxunhuang comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus AT juankang comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus AT yuanhuang comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus AT hongren comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus AT keyueding comparisonoferrorcorrectionalgorithmsforiontorrentpgmdataapplicationtohepatitisbvirus
_version_	1718393972804550656

Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus

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