Atropos

Introduction

Atropos is a tool for specific, sensitive, and speedy trimming of NGS reads.

For more information, please check its website: https://biocontainers.pro/tools/atropos and its home page on Github.

Versions

• 1.1.17

• 1.1.31

Commands

• atropos

Module

You can load the modules by:

module load biocontainers
module load atropos

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 Atropos on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=atropos
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers atropos

atropos --threads 4  \
    -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTTA \
    -o trimmed1.fq.gz -p trimmed2.fq.gz \
    -pe1 SRR13176582_1.fastq -pe2 SRR13176582_2.fastq