Medaka

Introduction

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

For more information, please check:

Docker hub: https://hub.docker.com/r/ontresearch/medaka

Home page: https://github.com/nanoporetech/medaka

Versions

• 1.11.1

Commands

• medaka

• medaka_consensus

• medaka_counts

• medaka_data_path

• medaka_haploid_variant

• medaka_version_report

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=medaka
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load medaka/XXXX ### you can run *module avail medaka* to check all available versions