====== medaka ======
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.

  * Latest Version: 0.8.2
  * Added: September, 2019
  * Link: https://github.com/nanoporetech/medaka

===== Usage =====
Show all available versions of medaka:
<code>$ module avail medaka</code>

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

<code>$ module load medaka/0.8.2
$ medaka</code>

===== Installation =====
Notes from the sysadmin during installation:

<code>$ 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 </code>

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