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