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Peer-reviewedCC BYBioinformatics

Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing

  • Sebastian Beier1
  • Anthony Bolger1
  • Marie Bolger1
  • Rainer Schwacke1
  • Björn Usadel2,1
  1. 1Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, BIOSC, Forschungszentrum Jülich , Wilhelm Johnen Straße , Jülich, 52425,
  2. 2Faculty of Mathematics and Natural Sciences, Institute for Biological Data Science, CEPLAS, Heinrich-Heine University Düsseldorf , Universitätsstr. 1 , Düsseldorf, 40225,
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Abstract

MOTIVATION: Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution. RESULTS: We present the substantial updates to Trimmomatic over the past decade. Key enhancements include a robust multithreading model for high-performance parallel processing, parallel GZIP/BZIP2 compression, and a suite of new trimming and filtering steps to provide users with more flexible quality control. Usability has been significantly improved through automatic PHRED encoding detection and simplified file handling. The codebase has also been modernized including Maven support, and continuous integration to ensure long-term sustainability and community contributions. These updates solidify Trimmomatic's role as an efficient, flexible, and essential tool in modern bioinformatics pipelines. AVAILABILITY: Trimmomatic remains open-source under the GPL V3 license, with the latest version available at https://github.com/usadellab/Trimmomatic and also on our website https://www.plabipd.de/trimmomatic_main.html (DOI: https://doi.org/10.5281/zenodo.18678155).

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Cite

BibTeXRIS
BibTeX
@article{beier2026trimmomatic,
  title = {{Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing}},
  author = {Sebastian Beier and Anthony Bolger and Marie Bolger and Rainer Schwacke and Björn Usadel},
  journal = {Bioinformatics},
  year = {2026},
  month = may,
  doi = {10.1093/bioinformatics/btag331},
  url = {https://doi.org/10.1093/bioinformatics/btag331},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing
AU  - Sebastian Beier
AU  - Anthony Bolger
AU  - Marie Bolger
AU  - Rainer Schwacke
AU  - Björn Usadel
PY  - 2026
DA  - 2026/05/20
JO  - Bioinformatics
DO  - 10.1093/bioinformatics/btag331
UR  - https://doi.org/10.1093/bioinformatics/btag331
AB  - MOTIVATION: Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution. RESULTS: We present the substantial updates to Trimmomatic over the past decade. Key enhancements include a robust multithreading model for high-performance parallel processing, parallel GZIP/BZIP2 compression, and a suite of new trimming and filtering steps to provide users with more flexible quality control. Usability has been significantly improved through automatic PHRED encoding detection and simplified file handling. The codebase has also been modernized including Maven support, and continuous integration to ensure long-term sustainability and community contributions. These updates solidify Trimmomatic's role as an efficient, flexible, and essential tool in modern bioinformatics pipelines. AVAILABILITY: Trimmomatic remains open-source under the GPL V3 license, with the latest version available at https://github.com/usadellab/Trimmomatic and also on our website https://www.plabipd.de/trimmomatic_main.html (DOI: https://doi.org/10.5281/zenodo.18678155).
SN  - 1367-4803
SN  - 1367-4811
ER  -