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Publication . Article . 2014

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger; Marc Lohse; Bjoern Usadel;
Open Access
English
Published: 01 Apr 2014
Publisher: Oxford Univ. Press
Country: Germany
Abstract

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: ed.nehcaa-htwr.1oib@ledasu Supplementary information: Supplementary data are available at Bioinformatics online.

Subjects by Vocabulary

Dewey Decimal Classification: ddc:004

Microsoft Academic Graph classification: Computer science Data science Flexibility (engineering) ATAC-seq Database computer.software_genre computer De novo transcriptome assembly Value (computer science) Index (publishing) Sequence assembly Phylogenomics Trimmer

Subjects

Original Papers, Genome Analysis, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability

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Bioinformatics
Article . 2014
Providers: PubMed Central
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