Afterqc

Introduction

Afterqc is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer.

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

Versions

  • 0.9.7

Commands

  • after.py

Module

You can load the modules by:

module load biocontainers
module load afterqc

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 blobtools on our our clusters:

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

module --force purge
ml biocontainers afterqc

after.py -1 SRR11941281_1.fastq.paired.fq  -2 SRR11941281_2.fastq.paired.fq