ArticleBioinformatics (Oxford, England)2026
Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Impact of hepatitis E virus host- and virus-derived insertions on the antiviral response in primary human hepatocytes.bioRxiv : the preprint server for biology · 2026Article
- Combined Transcriptomic and Histological Profiling Uncover Hepatic Regulatory Hierarchy of TriploidBiology · 2026Article
- The HD-Zip II Transcription FactorAntioxidants (Basel, Switzerland) · 2026Article
- The complete and annotated mitochondrial genome ofF1000Research · 2026Article
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Authors and funding
5 authors.
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Abstract
motivationTrimmomatic 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.
resultsWe 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.