nanofilt
Link to section 'Introduction' of 'nanofilt' Introduction
Nanofilt
is a tool for filtering and trimming of Oxford Nanopore Sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/nanofilt and its home page on Github.
Link to section 'Versions' of 'nanofilt' Versions
- 2.8.0
Link to section 'Commands' of 'nanofilt' Commands
- NanoFilt
Link to section 'Module' of 'nanofilt' Module
You can load the modules by:
module load biocontainers
module load nanofilt
Link to section 'Example job' of 'nanofilt' 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 Nanofilt on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nanofilt
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers nanofilt
NanoFilt -q 12 --headcrop 75 reads.fastq | gzip > trimmed-reads.fastq.gz