Fastq-scan

Introduction

Fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/fastq-scan

Home page: https://github.com/rpetit3/fastq-scan

Versions

• 1.0.0

Commands

• fastq-scan

Module

You can load the modules by:

module load biocontainers
module load fastq-scan

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 fastq-scan on our clusters:

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

module --force purge
ml biocontainers fastq-scan

cat example-q33.fq | fastq-scan -g 150000