Pychopper¶
Introduction¶
Pychopper is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/pychopper
Home page: https://github.com/nanoporetech/pychopper
Versions¶
2.5.0
Commands¶
cdna_classifier.py
Module¶
You can load the modules by:
module load biocontainers
module load pychopper
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 pychopper on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pychopper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers pychopper