Since its introduction in 2014, Trimmomatic has established itself as a gold standard for the preprocessing of next-generation sequencing (NGS) reads. Developed at the Institute of Bio- and Geosciences (IBG-4: Bioinformatics) at Forschungszentrum Jülich, the tool has been part of the de.NBI service portfolio from the very beginning, hosted by the German Crop BioGreenformatics Network (GCBN). Over the past decade, it has become one of the most widely used tools in the bioinformatics community, cited over 50,000 times and integrated into countless analysis pipelines worldwide.
Now, a comprehensive update has been published in the journal Bioinformatics (Oxford University Press): "Trimmomatic: A decade of feature-rich, high-performance NGS read preprocessing" by Sebastian Beier, Anthony M. Bolger, Marie E. Bolger, Rainer Schwacke, and Björn Usadel. The paper documents the substantial evolution of the tool from its original release to the current version v0.40, ensuring that Trimmomatic remains fit for the demands of modern large-scale sequencing projects.
A tool built for today's sequencing scale
The sheer volume of sequencing data has grown exponentially since 2014, with platforms like the Illumina NovaSeq series generating terabytes of data in a single run. To address this, Trimmomatic v0.40 introduces a high-performance multithreading engine delivering up to a 17-fold speedup, complemented by parallel GZIP/BZIP2 compression that resolves what had become the primary I/O bottleneck at high thread counts, yielding an additional 5-fold improvement in compressed output speed.
The trimming toolkit has also been significantly expanded. New steps include HEADCROP and TAILCROP for precise removal of UMI sequences and custom barcodes, AVGQUAL for filtering globally poor- quality reads, and BASECOUNT for enforcing post-trimming length thresholds. Automatic detection of PHRED quality score encoding and a built-in paired-end integrity validator further improve reliability in automated pipeline environments.
Best-in-class trimming accuracy
A comprehensive benchmark against five widely used tools (fastp, RabbitTrim, BBDuk, Skewer, and Cutadapt) showed that Trimmomatic's palindrome-based adapter trimming algorithm remains the most accurate available. On a complex plant (Manihot esculenta) dataset, Trimmomatic left only 14 true residual adapter reads, compared to 810 for fastp and 23,874 for Cutadapt. On a human dataset from the Genome-In-A-Bottle project, Trimmomatic left zero residual adapters. In terms of speed, Trimmomatic v0.40 is now fully competitive with highly optimised C++ tools.
Sustainable and accessible
To ensure long-term sustainability and ease of use, the codebase has been modernised with Maven build support and continuous integration. Trimmomatic is now officially distributed via Bioconda and as Docker and Singularity container images, making reproducible installation straightforward for all users. It remains fully open-source under the GPL v3 license.
Trimmomatic v0.40 is available at https://github.com/usadellab/Trimmomatic, https://www.plabipd.de/trimmomatic_main.html, and via the de.NBI service portal.
Read the full publication: https://doi.org/10.1093/bioinformatics/btag331