====== 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: 1.12.1
  * Added: September, 2019
  * Updated: May, 2025
  * Link: https://github.com/nanoporetech/medaka

===== Usage =====

Show which versions are available:
<code>$ module avail medaka</code>

Load one version into your environment and run it:

<code>$ module load medaka/1.12.1
$ medaka -h</code>

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

<code>$ module load python/3.10
$ sudo mkdir -p /export/apps/medaka/1.12.1/.venv
$ sudo chown aorth /export/apps/medaka/1.12.1/.venv
$ python -m venv /export/apps/medaka/1.12.1/.venv
$ source /export/apps/medaka/1.12.1/.venv/bin/activate
$ python -m pip install -U pip setuptools wheel
$ python -m pip install medaka==1.12.1
$ sudo chown -R root:root /export/apps/medaka/1.12.1</code>