Loading Bowtie2

  • modulebowtie2 (default: 2.5.4)
Tip: load modules inside your SLURM job script, not just on the login node, so compute nodes see the same environment. Verify with which after loading.

Commands

  • -x Path to the index for the reference genome
  • -1 File with mate 1 reads (paired-end)
  • -2 File with mate 2 reads (paired-end)
  • -U File with unpaired reads (single-end)
  • -S Output SAM file (default: stdout)
  • -p/--threads Number of parallel search threads (default: 1)
  • --localLocal alignment; ends might be soft clipped
  • --end-to-endEnd-to-end alignment (default)
  • -k Report up to alignments per read

Example usage

Load Bowtie2

module load bowtie2

Load a specific version

module load bowtie2/<version>

Single-end alignment

bowtie2 -p 8 -x /path/to/reference/genome -U sample.fastq -S output.sam

SLURM job script (paired-end alignment)

#!/bin/bash
#SBATCH --job-name=bowtie2_align
#SBATCH --output=bowtie2_align_%j.out
#SBATCH --error=bowtie2_align_%j.err
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH -p short-40core
#SBATCH --ntasks=40

module load bowtie2

INDEX="/path/to/reference/genome"
READS1="/path/to/sample_1.fastq"
READS2="/path/to/sample_2.fastq"
OUTPUT="/path/to/output.sam"

bowtie2 -p $SLURM_CPUS_PER_TASK -x $INDEX -1 $READS1 -2 $READS2 -S $OUTPUT

Availability

Bowtie2 is available on: SeaWulf, ClinWulf.