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Trimmomatic

Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, pair-aware preprocessing tool, optimized for Illumina next-generation sequencing (NGS) data. The software includes several processing steps for read trimming and filtering. It uses a pipeline-based architecture, allowing individual ‘steps’ (adapter removal, quality filtering, etc.) to be applied to each read/read pair, in the order specified by user.

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2 user reviews

2 user reviews

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lshepard

Excellent tool for trimming fastq files from Illumina for several NGS applications.

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tnov

Very useful Java tool for adapater trimming, low quality sequence removal, etc.. We are using it almost daily in our DNASeq/RNASeq pipelines.

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Trimmomatic versioning

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Trimmomatic classification

Trimmomatic specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Biological technology:
Illumina
Programming languages:
Java
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.36.zip
Galaxy:
https://toolshed.g2.bx.psu.edu/repository?repository_id=ef9e620e9ac844b3
Conda:
https://bioconda.github.io/recipes/trimmomatic/README.html
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
0.36
Maintained:
Yes
Debian:
https://packages.qa.debian.org/t/trimmomatic.html

Trimmomatic support

Documentation

Maintainer

  • Anthony Bolger <>

Credits

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Publications

Institution(s)

Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Golm,Institut für Biologie I, RWTH Aachen, Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany

Funding source(s)

Supported by the BMBF through grants 0315702F, 0315961 and 0315049A and BLE/BMELV
Verbundprojekt: G 127/10 IF.

Link to literature

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