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Trimmomatic: a flexible trimmer for Illumina sequence data.

Anthony M Bolger¹, Marc Lohse², Bjoern Usadel¹

¹Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany.

Bioinformatics (Oxford, England)

|April 4, 2014

Summary

This summary is machine-generated.

Trimmomatic is a new next-generation sequencing (NGS) preprocessing tool that efficiently handles paired-end data. It offers superior performance and flexibility compared to existing tools for various bioinformatics tasks.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Existing next-generation sequencing (NGS) read preprocessing tools lacked flexibility, efficient paired-end data handling, and high performance.
A need was identified for a more capable tool to meet specific NGS data processing requirements.

Purpose of the Study:

To develop a novel NGS read preprocessing tool named Trimmomatic.
To enhance flexibility and efficiency in handling paired-end sequencing data.

Main Methods:

Developed Trimmomatic, a Java-based, cross-platform preprocessing tool.
Implemented features for flexible and accurate handling of paired-end NGS data.

Main Results:

Trimmomatic demonstrated competitive or superior performance compared to existing tools across various scenarios.
The tool's value was validated for both reference-based and reference-free bioinformatics tasks.
Trimmomatic provides flexible and efficient preprocessing for NGS data.

Conclusions:

Trimmomatic offers a flexible and high-performance solution for NGS read preprocessing.
The tool effectively addresses limitations of previous preprocessing methods, particularly for paired-end data.
Trimmomatic is a valuable asset for bioinformatics analyses requiring robust read preprocessing.