trimmomatic

Version:

0.39

Category:

bio

Cluster:

Loki

Author / Distributor

http://www.usadellab.org/cms/?page=trimmomatic

Description

Trimmomatic is a flexible and efficient read trimming tool for Illumina NGS data. It is designed to remove adapters, trim low-quality bases, and filter out poor reads before alignment and downstream analysis.

Version 0.39 is a stable release with support for both single-end and paired-end read trimming, multithreading, and customizable pipelines.

Typical use cases:

  • Adapter clipping using built-in Illumina or custom FASTA files

  • Leading/trailing quality trimming

  • Sliding window quality trimming

  • Minimum length filtering

Trimmomatic is written in Java and operates via command-line.

Documentation

Usage: java -jar trimmomatic-0.39.jar <SE or PE> <input/output files> <options>

Example:
PE -phred33 input_forward.fq input_reverse.fq \
    output_forward_paired.fq output_forward_unpaired.fq \
    output_reverse_paired.fq output_reverse_unpaired.fq \
    ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Common steps:
  ILLUMINACLIP:<fasta>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
  LEADING:<quality>           Trim low-quality bases from the start
  TRAILING:<quality>          Trim low-quality bases from the end
  SLIDINGWINDOW:<size>:<quality>
  MINLEN:<length>             Discard reads shorter than specified

Help:
  java -jar trimmomatic-0.39.jar --help

Examples/Usage

  • Load the module:

$ module load bio/Trimmomatic/0.39

  • Run Trimmomatic on paired-end reads:

$ java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar PE \
  -phred33 reads_R1.fq reads_R2.fq \
  trimmed_R1_paired.fq trimmed_R1_unpaired.fq \
  trimmed_R2_paired.fq trimmed_R2_unpaired.fq \
  ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-PE.fa:2:30:10 \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

  • Run Trimmomatic on single-end reads:

$ java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar SE \
  -phred33 reads.fq trimmed_reads.fq \
  ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-SE.fa:2:30:10 \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

  • Unload the module:

$ module unload bio/Trimmomatic/0.39

Installation

Source code is obtained from trimmomatic