ConDeTri--a content dependent read trimmer for Illumina data.

<h4>Unlabelled</h4>During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in s...

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Autores principales:	Linnéa Smeds, Axel Künstner
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/85405a63c2f24223ad5311a7a4573998
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spelling	oai:doaj.org-article:85405a63c2f24223ad5311a7a45739982021-11-18T07:36:08ZConDeTri--a content dependent read trimmer for Illumina data.1932-620310.1371/journal.pone.0026314https://doaj.org/article/85405a63c2f24223ad5311a7a45739982011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22039460/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Unlabelled</h4>During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data.<h4>Availability and implementation</h4>Freely available on the web at http://code.google.com/p/condetri.Linnéa SmedsAxel KünstnerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e26314 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Linnéa Smeds Axel Künstner ConDeTri--a content dependent read trimmer for Illumina data.
description	<h4>Unlabelled</h4>During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data.<h4>Availability and implementation</h4>Freely available on the web at http://code.google.com/p/condetri.
format	article
author	Linnéa Smeds Axel Künstner
author_facet	Linnéa Smeds Axel Künstner
author_sort	Linnéa Smeds
title	ConDeTri--a content dependent read trimmer for Illumina data.
title_short	ConDeTri--a content dependent read trimmer for Illumina data.
title_full	ConDeTri--a content dependent read trimmer for Illumina data.
title_fullStr	ConDeTri--a content dependent read trimmer for Illumina data.
title_full_unstemmed	ConDeTri--a content dependent read trimmer for Illumina data.
title_sort	condetri--a content dependent read trimmer for illumina data.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/85405a63c2f24223ad5311a7a4573998
work_keys_str_mv	AT linneasmeds condetriacontentdependentreadtrimmerforilluminadata AT axelkunstner condetriacontentdependentreadtrimmerforilluminadata
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ConDeTri--a content dependent read trimmer for Illumina data.

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