Software: Fastq-scan
Description
Fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.
Available Versions
| Unspecified: | 1.0.0 |
|---|
Docker hub: https://hub.docker.com/r/staphb/fastq-scan
Home page: https://github.com/rpetit3/fastq-scan
Commands
- fastq-scan
Module
You can load the modules by:
module load biocontainers
module load fastq-scan
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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