Medaka
Description
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.
License
Mozilla Public License Version 2.0
Usage
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/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
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
Documentation
https://github.com/nanoporetech/medaka#usage