Journal
BIOINFORMATICS
Volume 30, Issue 15, Pages 2114-2120Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu170
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Funding
- BMBF [0315702F, 0315961, 0315049A]
- BLE/BMELV [G 127/10 IF]
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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.
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