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PLoS One. 2013 Dec 23;8(12):e85024. doi: 10.1371/journal.pone.0085024. eCollection 2013.

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

Author information

1
Institute of Applied Genomics, Udine, Italy.
2
IGA Technology Services, Udine, Italy.
3
Institute of Applied Genomics, Udine, Italy ; Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America.

Abstract

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.

PMID:
24376861
PMCID:
PMC3871669
DOI:
10.1371/journal.pone.0085024
[Indexed for MEDLINE]
Free PMC Article

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