usadellab/Trimmomatic: v0.40

Beier, Sebastian; Bolger, Anthony M.; Bolger, Marie; Schwacke, Rainer; Usadel, Björn

doi:10.5281/zenodo.18678155

Published February 18, 2026 | Version v1

Software Open

usadellab/Trimmomatic: v0.40

1. Forschungszentrum Jülich
2. Heinrich Heine University Düsseldorf

This release introduces several new features focused on usability and performance, as well as a complete modernization of the build and testing process.

New Features

Advanced Compression Control: Users can now fine-tune the output compression.
- Added parallel compression for GZip and BZip2.
- Added -compressBlock (default) and -compressStream options to control the compression mode.
- Added -compressLevel option to specify the compression level for GZip and BZip2 (from 1=fastest to 9=best).
Automatic Adapter File Discovery: The ILLUMINACLIP step is now more user-friendly. If a full path to the adapter FASTA file is not provided, Trimmomatic will automatically search for the file in the following order:
1. The adapters subdirectory located next to the Trimmomatic .jar file.
2. The current working directory.
  This removes the need to hard-code paths for the standard adapter files included with the distribution.
Poly-G Detection: Added Poly-G adapter sequences to target and remove G-tail artifacts, which are common in Illumina NextSeq and NovaSeq two-color chemistry data.

Build and CI/CD Improvements

Maven Integration: The project has been completely migrated to a Maven build system. This standardizes the build process, makes dependency management automatic, and simplifies compiling the project from source.
Added GitHub Actions workflows to automate key development processes:
- Automated Testing: Unit tests (JUnit) are now automatically run on every push to ensure code quality and stability.
- Automated Docker Builds: A Docker container is automatically built and published with each new release, simplifying deployment for users.

Docker Support

With each release, a Docker container is automatically built and published to the GitHub Container Registry. You can pull the image for this release using the following command:

docker pull ghcr.io/usadellab/trimmomatic:v0.40

Files

Trimmomatic-0.40.zip

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Trimmomatic-0.40.zip md5:f34f93942f3472de0dd2a1b834f56372	108.0 kB	Preview Download

Additional details

Is supplement to: Software: https://github.com/usadellab/Trimmomatic/tree/v0.40 (URL)

German Network for Bioinformatics Infrastructure – de.NBI
ELIXIR Germany

Repository URL: https://github.com/usadellab/Trimmomatic/
Programming language: Java
Development Status: Active

Anthony M. Bolger, Marc Lohse, Bjoern Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, Volume 30, Issue 15, August 2014, Pages 2114–2120, https://doi.org/10.1093/bioinformatics/btu170

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The license does NOT apply to the sequence of the Illumina sequences contained in the software. THE ILLUMINA sequences (adapters) etc REMAIN COPYRIGHTED and owned by Illumina and are used in trimmomatic by permission. The software and sourecode are licensed by the .... GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. 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Technical metadata

Created: February 18, 2026
Modified: February 18, 2026

New Features

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Trimmomatic-0.40.zip

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usadellab/Trimmomatic: v0.40

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Description

New Features

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Trimmomatic-0.40.zip

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