Cutadapt

Introduction

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

For more information, please check its website: https://biocontainers.pro/tools/cutadapt and its home page: https://cutadapt.readthedocs.io/en/stable/.

Versions

3.4
3.7

Commands

cutadapt

Module

You can load the modules by:

module load biocontainers
module load cutadapt

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Cutadapt on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cutadapt
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cutadapt


cutadapt -a AACCGGTT -o output.fastq input.fastq