pycoqc
Link to section 'Introduction' of 'pycoqc' Introduction
Pycoqc is a tool that computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/pycoqc and its home page on Github.
Link to section 'Versions' of 'pycoqc' Versions
- 2.5.2
Link to section 'Commands' of 'pycoqc' Commands
- pycoQC
- python
- python3
Link to section 'Module' of 'pycoqc' Module
You can load the modules by:
module load biocontainers
module load pycoqc
Link to section 'Example job' of 'pycoqc' 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 Pycoqc on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pycoqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers pycoqc
pycoQC \
-f Albacore-1.2.1_basecall-1D-DNA_sequencing_summary.txt\
-o Albacore-1.2.1_basecall-1D-DNA.html \
--quiet