đź•‘ 10:30 CET
đź“… April 14, 2023
đź“Ť Online
Title: Using connected subgraphs of the De Bruijn graph as variants in bacterial GWAS
Abstract:
Genome wide association studies (GWAS) aim at finding genetic variants associated with a trait. When dealing with bacterial genomes one often relies on k-mers, whose presence in a genome can denote variants ranging from SNPs to mobile genetic elements. However, many k-mers can sometimes represent the same gene, leading to diluted effects. Here we propose to build more flexible variants by testing closed connected subgraphs of the De Bruijn graph defined over genomic k-mers. We show how to overcome the computational and statistical issues arising when testing so many elements by using Tarone’s trick and a reverse search strategy.
Recorded Video: https://youtu.be/naXW1E9a6ew