Trimmomatic - NGS Read Trimmer
Trimmomatic is a highly flexible and efficient tool for quality trimming and preprocessing of Illumina sequencing reads. It removes adapters, filters low-quality bases, and cleans raw data prior to downstream analyses. Designed for both single-end and paired-end datasets, Trimmomatic is widely used as a standard first step in NGS workflows.
Key Benefits
- High-performance trimming for large sequencing datasets.
- Modular, customizable pipeline with user-defined trimming steps.
- Adapter clipping using built-in or user-provided adapter files.
- Improves read quality and reduces downstream artifacts.
- Paired-end aware: keeps read pairing intact throughout processing.
Features
- Adapter removal and sequence clipping.
- Quality-based trimming at read ends or sliding windows.
- Filtering of short or low-quality reads.
- Support for gzip-compressed input/output.
- Straightforward integration into automated workflows and HPC systems.
Applications
- Preprocessing of Illumina NGS reads for metagenomics, genomics, RNA-seq, and amplicon sequencing.
- Increasing assembly accuracy and mapping performance by removing poor-quality data.
- Standard component in reproducible, large-scale bioinformatics pipelines.
Intended Use
Trimmomatic is ideal for bioinformaticians, genomics researchers, and sequencing facilities who require a robust, configurable read-cleaning tool as part of their NGS preprocessing workflow.
Funding: Maintenance partly funded by de.NBI