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
- 1.0.0
- fastq-scan
You can load the modules by:
module load biocontainers module load fastq-scan
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