Trimmomatic

Trimmomatic trims adapters and low-quality bases from Illumina FASTQ files (single-end or paired-end).


Module	`genom/trimmomatic/0.39`
Depends on	`lang/java` (loaded automatically)
Command	`trimmomatic` (wrapper around the JAR)
Adapters	`$TRIMMOMATIC_DIR/adapters`

Load

$ module load genom/trimmomatic

Example (paired-end)

Cap Java threads to the Slurm allocation. Without -threads, the JVM may try to use every CPU on the node.

trimmomatic.slurm

#!/bin/bash
#SBATCH -J trimmomatic
#SBATCH -c 8
#SBATCH --mem-per-cpu=2G
#SBATCH -t 04:00:00
#SBATCH -o %x-%j.out

module load genom/trimmomatic
export MALLOC_ARENA_MAX=2
trimmomatic PE -threads "$SLURM_CPUS_PER_TASK" \
  "$DATA_DIR/reads/R1.fq.gz" "$DATA_DIR/reads/R2.fq.gz" \
  "$SCRATCH_DIR/trim/R1.paired.fq.gz" "$SCRATCH_DIR/trim/R1.unpaired.fq.gz" \
  "$SCRATCH_DIR/trim/R2.paired.fq.gz" "$SCRATCH_DIR/trim/R2.unpaired.fq.gz" \
  ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Adapter FASTA files shipped with the install:

TruSeq3-PE.fa, TruSeq3-PE-2.fa, TruSeq3-SE.fa
TruSeq2-PE.fa, TruSeq2-SE.fa
NexteraPE-PE.fa

Tip

MALLOC_ARENA_MAX=2 plus -threads "$SLURM_CPUS_PER_TASK" avoids the JVM reserving huge virtual memory on shared nodes. See the Trimmomatic HPC note.

Single-end mode is trimmomatic SE .... Check trimmed reads with FastQC, then align with STAR.

TElocal VASP