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Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. It provides state-of-the-art results outperforming sequence-graph based methods and signal-based methods, whilst also being faster.


Mozilla Public License Version 2.0


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of medaka and load default version of medaka as

module avail medaka/ # list available modules
module load medaka   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail medaka

and choose explicit version you want to use.

CPU version of Medaka is available as a Conda environment. Module with suffix -gpu supports GPU acceleration.

$ module add medaka-1.6.0-gpu
$ source /software/medaka/1.6.0_gpu/venv/bin/activate
(medaka) $ medaka_consensus -i <fasta> -d <assembly> ...
(medaka) $ deactivate