Organised by Biodiversity Genomics Academy

Introduction

Biodiversity Genomics Academy 2024 (BGA24) is a series of free, open to all, nline-only, short and interactive sessions on how to use the bioinformatics tools and approaches that underpin the Earth BioGenome Project and the field as a whole.

More information on our website.

Programme

  • Introduction to k-mer spectra, their interpretation and running GenomeScope (~30')
  • Ex. 1: Running and understanding genome models (~30')
  • Looking under the hood of the GenomeScope model (~20')
  • Ex. 2: Running GenomeScope-like model yourself in R; Using GenomeTelescope package (~20')
  • Discussion/Interpretation of wild k-mer spectra (~20')
    • We will bring a bunch of examples; but feel free to bring your own wild k-mer spectrum to share with others!

Description

By the end of this session you will be able to:

  1. Appreciate the art of the k-mer spectra gazing
  2. Understand the idea behind genomescope model and its assumptions
  3. Generate k-mer spectrum from a read set
  4. Run GenomeScope in command-line and web-server
  5. (if everything goes well) Create your own GenomeScope-like extended versions;

Prerequisites

  1. Basics knowledge of genomics
  2. Be ready for some non-linear regression
  3. (optional) familiarity with k-mers (Some materials developed by ourselves: https://github.com/KamilSJaron/oh-know/wiki)
  4. (optional) Read relevant sections of https://www.nature.com/articles/s41467-020-14998-3