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