nanopolish
Link to section 'Introduction' of 'nanopolish' Introduction
Nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/nanopolish and its home page on Github.
Link to section 'Versions' of 'nanopolish' Versions
- 0.13.2
- 0.14.0
Link to section 'Commands' of 'nanopolish' Commands
- nanopolish
Link to section 'Module' of 'nanopolish' Module
You can load the modules by:
module load biocontainers
module load nanopolish
Link to section 'Example job' of 'nanopolish' 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 Nanopolish on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nanopolish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers nanopolish
nanopolish index -d fast5_files/ reads.fasta
nanopolish variants --consensus \
-o polished.vcf -w "tig00000001:200000-202000" \
-r reads.fasta -b reads.sorted.bam -g draft.fa