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Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1.

Trimmomatic: a flexible trimmer for Illumina sequence data.

Author information

1
Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany.
2
Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, 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:

usadel@bio1.rwth-aachen.de

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
24695404
PMCID:
PMC4103590
DOI:
10.1093/bioinformatics/btu170
[Indexed for MEDLINE]
Free PMC Article

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