longqc
Link to section 'Introduction' of 'longqc' Introduction
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
Docker hub: https://hub.docker.com/r/cymbopogon/longqc
Home page: https://github.com/yfukasawa/LongQC
Link to section 'Versions' of 'longqc' Versions
- 1.2.0c
Link to section 'Commands' of 'longqc' Commands
- longQC.py
Link to section 'Module' of 'longqc' Module
You can load the modules by:
module load biocontainers
module load longqc
Link to section 'Example job' of 'longqc' Example job
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