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Pipelines for NGS, imputation, gwas, ...
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compute5 Remove all hardcoded paths from paramters.csv. Fixed all protocols to…

MOLGENIS pipelines


This repository contains the following pipelines:

  • Alignment
  • Imputation
  • GWAS
  • RNA-seq (Experimental)

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 visit

Step 1: download Molgenis Compute

# Download the latest MOLGENIS Compute from
# Currently (March 2013)

# create dir
mkdir mycompute
cd mycompute

# download
unzip molgenis_compute-\<version>.zip
mv molgenis_compute-\<version>/* .  

# test  

Step 2: clone this repo

# For read/write access:
git clone
# Alternatively to only download the pipelines use:
unzip master
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