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:
BioContainers: https://biocontainers.pro/tools/cutadapt
Home page: https://cutadapt.readthedocs.io/en/stable/

Versions

3.4
3.7

Commands

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=cutadapt
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load cutadapt/XXXX ### you can run *module avail cutadapt* to check all available versions

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