chopper
Link to section 'Introduction' of 'chopper' Introduction
Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file. Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.
BioContainers: https://biocontainers.pro/tools/chopper
Home page: https://github.com/wdecoster/chopper
Link to section 'Versions' of 'chopper' Versions
- 0.2.0
Link to section 'Commands' of 'chopper' Commands
- chopper
Link to section 'Module' of 'chopper' Module
You can load the modules by:
module load biocontainers
module load chopper
Link to section 'Example job' of 'chopper' 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 chopper on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=chopper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers chopper