Genome profiling using GenomeScope¶
This session is part of Biodiversity Genomics Academy 2023
- Introduction to k-mer spectra, their interpretation and running GenomeScope (lecture by Lucía, ~30')
- Ex. 1: Running and understanding genome models (~30')
- Looking under the hood of the GenomeScope model (lecture by Kamil, ~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 spoectrum to share with others!
By the end of this session you will be able to:
- Appreciate the art of the k-mer spectra gazing
- Understand the idea behind genomescope model and its assumptions
- Generate k-mer spectrum from a read set
- Run GenomeScope in command-line and web-server
- (if everything goes well) Create your own GenomeScope-like extended versions;
- Basics knowledge of genomics
- Be ready for some non-linear regression
- (optional) familiarity with k-mers (Some materials developed by ourselves: https://github.com/KamilSJaron/oh-know/wiki)
- (optional) Read relevant sections of https://www.nature.com/articles/s41467-020-14998-3
Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above
You will get the most out of this session if you meet the prerequisites above.
Please also read the description carefully to see if this session is relevant to you.
If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.