Medaka 2016

From HPC users
Revision as of 14:50, 18 November 2019 by Schwietzer (talk | contribs) (→‎Installed version(s))
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search


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 faster¹.

Installed version(s)

This version is installed and currently available on environment hpc-env/6.4:


Using medaka

If you want to find out more about medaka on the HPC cluster, you can use the command

module spider medaka

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env 6.4
module load medaka

Always remember: this command is case sensitive!

To get a short description on how to use the medaka command, you can use the help function:

medaka --help

With this command, you can check whether all dependencies are propperly loaded/installed:



The full documentation can be found here.