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.

Versions

2.5.2

Commands

pycoQC
python
python3

Module

You can load the modules by:

module load biocontainers
module load pycoqc

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 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