Assessing genome conservation on pangenome graphs with PanSel
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Motivation
With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a reference genome, augmented with variations. However, this major change requires new tools adapted to this data structure. Among the numerous questions that can be addressed to a pangenome graph is the search for conserved or divergent genes.
Results
In this article, we present a new tool, named PanSel, which computes a conservation score for each segment of the genome, and finds genomic regions that are significantly conserved, or divergent. PanSel can be used on prokaryotes and eukaryotes, with a sequence identity not less than 98%.
Availability and implementation
PanSel, written in C++11 with no dependency, is available at https://github.com/mzytnicki/pansel.
