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Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing
Sebastian Beier1, Anthony M Bolger1, Marie E Bolger1
1Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, BIOSC, Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, 52425, Germany.
Bioinformatics (Oxford, England)
|May 24, 2026
Summary
Trimmomatic has been significantly updated to handle modern sequencing data. Enhancements include multithreading, new quality control features, and improved usability for bioinformatics pipelines.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Trimmomatic is a key tool for preprocessing high-throughput sequencing data.
- Increased data volume and complexity necessitate ongoing tool development.
Purpose of the Study:
- To detail substantial updates to Trimmomatic over the past decade.
- To highlight improvements in performance, flexibility, and usability.
Main Methods:
- Implemented a robust multithreading model for parallel processing.
- Integrated parallel GZIP/BZIP2 compression.
- Developed new trimming and filtering steps for quality control.
Main Results:
- Enhanced parallel processing capabilities for high-throughput data.
- Introduced flexible quality control options with new trimming/filtering steps.
- Improved usability through automatic PHRED encoding detection and simplified file handling.
- Modernized codebase with Maven support and continuous integration.
Conclusions:
- Updated Trimmomatic is an efficient, flexible, and essential tool for modern bioinformatics.
- Continuous development ensures Trimmomatic's long-term sustainability and community contribution.
