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

Show which versions are available:

$ module avail medaka

Load one version into your environment and run it:

$ module load medaka/1.12.1
$ medaka -h

Notes from the sysadmin during installation:

$ 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