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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)
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Summary

Trimmomatic has been significantly updated to handle modern sequencing data. Enhancements include multithreading, new quality control features, and improved usability for bioinformatics pipelines.

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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.