PangeBlocks: customized construction of pangenome graphs via maximal blocks.

ABSTRACT:

Background

The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization criterion and the set of feasible solutions. Current approaches build a pangenome graph with some heuristics, without assuming some explicit optimization criteria. Thus it is unclear how a specific optimization criterion affects the graph topology and downstream analysis, like read mapping and variant calling.

Results

In this paper, by leveraging the notion of maximal block in a Multiple Sequence Alignment (MSA), we reframe the pangenome graph construction problem as an exact cover problem on blocks called Minimum Weighted Block Co

SUBMITTER: Avila Cartes J 

PROVIDER: S-EPMC11533710 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature