DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing.
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. D...
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doaj-7b481c96c09940fdbe1107d5c6aa6ae72020-11-25T02:12:28ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01127e018146310.1371/journal.pone.0181463DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing.Byunghan LeeTaesup MoonSungroh YoonTsachy WeissmanWe consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms. Our experimental studies with real and simulated datasets suggest that the proposed DUDE-Seq not only outperforms existing alternatives in terms of error-correction capability and time efficiency, but also boosts the reliability of downstream analyses. Further, the flexibility of DUDE-Seq enables its robust application to different sequencing platforms and analysis pipelines by simple updates of the noise model. DUDE-Seq is available at http://data.snu.ac.kr/pub/dude-seq.http://europepmc.org/articles/PMC5531809?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Byunghan Lee Taesup Moon Sungroh Yoon Tsachy Weissman |
spellingShingle |
Byunghan Lee Taesup Moon Sungroh Yoon Tsachy Weissman DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. PLoS ONE |
author_facet |
Byunghan Lee Taesup Moon Sungroh Yoon Tsachy Weissman |
author_sort |
Byunghan Lee |
title |
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. |
title_short |
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. |
title_full |
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. |
title_fullStr |
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. |
title_full_unstemmed |
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. |
title_sort |
dude-seq: fast, flexible, and robust denoising for targeted amplicon sequencing. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms. Our experimental studies with real and simulated datasets suggest that the proposed DUDE-Seq not only outperforms existing alternatives in terms of error-correction capability and time efficiency, but also boosts the reliability of downstream analyses. Further, the flexibility of DUDE-Seq enables its robust application to different sequencing platforms and analysis pipelines by simple updates of the noise model. DUDE-Seq is available at http://data.snu.ac.kr/pub/dude-seq. |
url |
http://europepmc.org/articles/PMC5531809?pdf=render |
work_keys_str_mv |
AT byunghanlee dudeseqfastflexibleandrobustdenoisingfortargetedampliconsequencing AT taesupmoon dudeseqfastflexibleandrobustdenoisingfortargetedampliconsequencing AT sungrohyoon dudeseqfastflexibleandrobustdenoisingfortargetedampliconsequencing AT tsachyweissman dudeseqfastflexibleandrobustdenoisingfortargetedampliconsequencing |
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