longqc.rst

Longqc

Introduction ~~~~~~~~ LongQC is a tool for the data quality control of the PacBio and ONT long reads.

For more information, please check:
Docker hub: https://hub.docker.com/r/cymbopogon/longqc
Home page: https://github.com/yfukasawa/LongQC

Versions

• 1.2.0c

Commands ~~~~~~~ - longQC.py

Module

You can load the modules by:

module load biocontainers
module load longqc

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 longqc on our clusters:

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

module --force purge
ml biocontainers longqc

longQC.py sampleqc -x pb-rs2 -o out_dir seq.fastq