Cargando…

PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm

BACKGROUND: In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. RESULTS: Here, we pr...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Yun-Lung, Weng, Jui-Cheng, Hsiao, Chiung-Chih, Chou, Min-Te, Tseng, Chin-Wen, Hung, Jui-Hung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331701/
https://www.ncbi.nlm.nih.gov/pubmed/25707528
http://dx.doi.org/10.1186/1471-2105-16-S1-S2
_version_ 1782357762021261312
author Li, Yun-Lung
Weng, Jui-Cheng
Hsiao, Chiung-Chih
Chou, Min-Te
Tseng, Chin-Wen
Hung, Jui-Hung
author_facet Li, Yun-Lung
Weng, Jui-Cheng
Hsiao, Chiung-Chih
Chou, Min-Te
Tseng, Chin-Wen
Hung, Jui-Hung
author_sort Li, Yun-Lung
collection PubMed
description BACKGROUND: In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. RESULTS: Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested. CONCLUSIONS: PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online.
format Online
Article
Text
id pubmed-4331701
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-43317012015-03-19 PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm Li, Yun-Lung Weng, Jui-Cheng Hsiao, Chiung-Chih Chou, Min-Te Tseng, Chin-Wen Hung, Jui-Hung BMC Bioinformatics Proceedings BACKGROUND: In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. RESULTS: Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested. CONCLUSIONS: PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online. BioMed Central 2015-01-21 /pmc/articles/PMC4331701/ /pubmed/25707528 http://dx.doi.org/10.1186/1471-2105-16-S1-S2 Text en Copyright © 2015 Li et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Li, Yun-Lung
Weng, Jui-Cheng
Hsiao, Chiung-Chih
Chou, Min-Te
Tseng, Chin-Wen
Hung, Jui-Hung
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title_full PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title_fullStr PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title_full_unstemmed PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title_short PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
title_sort peat: an intelligent and efficient paired-end sequencing adapter trimming algorithm
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331701/
https://www.ncbi.nlm.nih.gov/pubmed/25707528
http://dx.doi.org/10.1186/1471-2105-16-S1-S2
work_keys_str_mv AT liyunlung peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm
AT wengjuicheng peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm
AT hsiaochiungchih peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm
AT chouminte peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm
AT tsengchinwen peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm
AT hungjuihung peatanintelligentandefficientpairedendsequencingadaptertrimmingalgorithm