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medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.


Show all available versions of medaka:

$ module avail medaka

Load one version into your environment and run it:

$ module load medaka/1.4.3
$ medaka -h


Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/medaka/1.4.3
$ sudo chown -R aorth:aorth /export/apps/medaka/1.4.3
$ module load python/3.7
$ python3 -m venv /export/apps/medaka/1.4.3
$ source /export/apps/medaka/1.4.3/bin/activate
$ pip install --upgrade pip setuptools
$ pip install medaka==1.4.3
$ sudo chown -R root:root /export/apps/medaka/1.4.3
medaka-software.txt · Last modified: 2021/08/25 12:15 by aorth