This repository contains the following pipelines:

  • Imputation

  • RNA-seq (Experimental)

It also contains pipelines with their own repo's like:

In addition it contains protocols that may be re-used between different (versions of a) pipeline(s).

How to get started

Below we explain (step 1) how to download and deploy Molgenis Compute. This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data. Next, we explain (step 2) how you can download even more pipelines and protocols by cloning this repo.

For a 'walkthrough' tutorial on Molgenis Compute, please go here

Step 1: download Molgenis Compute

create dir

mkdir mycompute
cd mycompute


tar -xzvf molgenis-compute-v16.11.1.tar.gz



Step 2: clone this repo

For read/write access:

git clone

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