Medaka

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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

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

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

Homepage

https://github.com/nanoporetech/medaka