medaka
Link to section 'Introduction' of 'medaka' Introduction
Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
Docker hub: https://hub.docker.com/r/ontresearch/medaka and its home page on Github.
Link to section 'Versions' of 'medaka' Versions
- 1.6.0
Link to section 'Commands' of 'medaka' Commands
- medaka
- medaka_consensus
- medaka_counts
- medaka_data_path
- medaka_haploid_variant
- medaka_version_report
Link to section 'Module' of 'medaka' Module
You can load the modules by:
module load biocontainers
module load medaka
Link to section 'Example job' of 'medaka' 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 Medaka on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=medaka
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers medaka