Medaka

Introduction

Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.

For more information, please check its | Docker hub: https://hub.docker.com/r/ontresearch/medaka and its home page on Github.

Versions

  • 1.6.0

Commands

  • medaka

  • medaka_consensus

  • medaka_counts

  • medaka_data_path

  • medaka_haploid_variant

  • medaka_version_report

Module

You can load the modules by:

module load biocontainers
module load medaka

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 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