Pan-genome de Bruijn graph using the bidirectional FM-index.

ABSTRACT:

Background

Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally reveals similarity and divergence within the pan-genome. Most state-of-the-art pan-genome graphs are represented explicitly in terms of nodes and edges. Recently, an alternative, implicit graph representation was proposed that builds directly upon the unidirectional FM-index. As such, a memory-efficient graph data structure is obtained that inherits the FM-index' backward search functionality. However, this representation suffers from a number of shortcomings in terms of functionality and algorithmic performance.

Results

We p

SUBMITTER: Depuydt L 

PROVIDER: S-EPMC10605969 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature