atropos
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'atropos' Versions
- 1.1.17
- 1.1.31
Link to section 'Commands' of 'atropos' Commands
- atropos
Link to section 'Module' of 'atropos' Module
You can load the modules by:
module load biocontainers
module load atropos
Link to section 'Example job' of 'atropos' Example job
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