ILRI Research Computing

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

====== 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: 1.4.3
  * Added: September, 2019
  * Updated: August, 2021
  * Link: https://github.com/nanoporetech/medaka

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

Load one version into your environment and run it:

<code>$ module load medaka/1.4.3
$ medaka -h</code>

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

<code>$ 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</code>