An extensive evaluation of read trimming effects on Illumina NGS data analysis.

Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analy...

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Autores principales:	Cristian Del Fabbro, Simone Scalabrin, Michele Morgante, Federico M Giorgi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/43e0dc820ed44c82ba28223aac613d29
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id	oai:doaj.org-article:43e0dc820ed44c82ba28223aac613d29
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spelling	oai:doaj.org-article:43e0dc820ed44c82ba28223aac613d292021-11-18T08:40:28ZAn extensive evaluation of read trimming effects on Illumina NGS data analysis.1932-620310.1371/journal.pone.0085024https://doaj.org/article/43e0dc820ed44c82ba28223aac613d292013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24376861/?tool=EBIhttps://doaj.org/toc/1932-6203Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.Cristian Del FabbroSimone ScalabrinMichele MorganteFederico M GiorgiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e85024 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Cristian Del Fabbro Simone Scalabrin Michele Morgante Federico M Giorgi An extensive evaluation of read trimming effects on Illumina NGS data analysis.
description	Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.
format	article
author	Cristian Del Fabbro Simone Scalabrin Michele Morgante Federico M Giorgi
author_facet	Cristian Del Fabbro Simone Scalabrin Michele Morgante Federico M Giorgi
author_sort	Cristian Del Fabbro
title	An extensive evaluation of read trimming effects on Illumina NGS data analysis.
title_short	An extensive evaluation of read trimming effects on Illumina NGS data analysis.
title_full	An extensive evaluation of read trimming effects on Illumina NGS data analysis.
title_fullStr	An extensive evaluation of read trimming effects on Illumina NGS data analysis.
title_full_unstemmed	An extensive evaluation of read trimming effects on Illumina NGS data analysis.
title_sort	extensive evaluation of read trimming effects on illumina ngs data analysis.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/43e0dc820ed44c82ba28223aac613d29
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An extensive evaluation of read trimming effects on Illumina NGS data analysis.

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