Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M Bolger, Marc Lohse, Bjoern Usadel, Anthony M Bolger, Marc Lohse, Bjoern Usadel
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.
© The Author 2014. Published by Oxford University Press.
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References
- Aronesty E. Comparison of sequencing utility programs. Open Bioinform. J. 2013;7:1–8.
- Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell. Bioinformatics. 2010;26:1669–1670.
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359.
- Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–1760.
- Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 2010;11:473–483.
- Li JW, et al. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Brief. Bioinform. 2013;14:548–555.
- Lindgreen S. AdapterRemoval: easy cleaning of next generation sequencing reads. BMC Res. Notes. 2012;5:337.
- Mardis ER. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 2008;9:387–402.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12.
- Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829.
Source: PubMed