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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 a particular version of medaka into your environment and run it:

$ module load medaka/0.8.2
$ medaka


Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/medaka/v0.8.2
$ sudo chown aorth /export/apps/medaka/v0.8.2
$ python3 -m venv /export/apps/medaka/v0.8.2
$ source /export/apps/medaka/v0.8.2/bin/activate
$ pip install --upgrade pip setuptools
$ pip install medaka
$ sudo chown -R root:root 

This uses the CentOS 7 system's Python 3.6 environment.

medaka-software.txt · Last modified: 2019/09/03 22:12 by aorth