The crunchomics compute cluster

The SILS and IBED institutes are maintaining a compute environment to allow researchers to run compute-intensive jobs.

For example, crunchomics can be used for:

  • Performing the bioinformatic parts of an RNA-seq analysis: mapping the reads to a genome reference, counting, etc.
  • Analysing the microbiome data coming from the sequencing of a gut microbiome,
  • Running Machine Learning analyses using R or Python.

First step: get an account

To get an account, please send your name, UvA net ID and affiliation to Wim de Leeuw by email (

Second step: read the Crunchomics documentation

The official Crunchomics official documentation lives here.

The documentation describes the crunchomics architecture, how to connect to the head node, how to run jobs using the workload manager SLURM and much more!

Third step: getting help 🙂

Option 1 (preferred):

  1. Join the Study Group Slack workspace by clicking here.
  2. Post your question in the #crunchomics channel.

Option 2: