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Mark Ravinet edited this page Jan 6, 2026 · 11 revisions

The Ecological & Evolutionary Genetics Group at UiO

Welcome to the wiki pages for the EEG group based at CEES, UiO. Here you will find all the information you need on samples available in the lab, protocols for performing analyses, our data storage policies and how to access the Saga HPC.

If you have any questions or need advice, please contact Mark!

Introductions and tutorials

  1. An Introduction to Unix - where to start if you're completely new!
  2. Going further with Unix - and if you want to develop more skills.
  3. Speciation Genomics - a crash course in using genomic data to study speciation and adaptation - many useful and relevant tutorials hosted here.
  4. Working with ebird data - a short series of tutorials for working with data from eBird.
  5. An introduction to using R for evolutionary genomics
  6. Modelling and spatial analysis - some notes and tutorials from a course from Sweden in 2023.

Important links and information

  1. The sparrow sample catalogue - NB: Access is restricted - you need to request access from Mark to be able to view this
  2. Group equipment list - As above, please ask for access if required
  3. Getting started with the HPC - our guide for working on the Saga HPC cluster.
  4. Working on the HPC - a short how-to-guide to slurm and submitting jobs.
  5. Requesting memory and CPUs during job submissions - a MUST READ guide for ensuring you request the right amount of resources
  6. Managing data - a guide to working with data within the sparrow project.
  7. Modules and installing - how to view and load modules.
  8. Running conda on the cluster - how to run conda using Saga modules.
  9. The sparrow style guide - guidelines for visualising data with custom palettes.
  10. A guide to sparrow genome resources - an explainer on the different genome assemblies, resources and how to switch between them

Tools and scripts

  1. Group repository for scripts and analyses - including the home of the Nextflow-based pipelines Erik has been working on.
  2. The group genotyping pipeline - the home of XENO - e__X__tremely __E__fficient genotyping pipeline for __N__on-model __O__rganisms a Nextflow-based genotyping pipeline for fast and efficient genotyping of multiple samples using GPUs
  3. Reproducible analysis pipelines - the home of RIPLEY - __R__eproducible __P__ipe__L__ines for __E__volutionary analy__Y__is - Nextflow-based workflows for producing standard analyses such as PCA, ADMIXTURE and mitochondrial analyses
  4. Shared group scripts - shareable scripts that group memmbers have writen and are happy to share.

Style guides and further information

See here for details on how to set colours for figures and plots.

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