arXiv (Cornell University)
Prefix-free graphs and suffix array construction in sublinear space
June 2023 • Andrej Baláž, Alessia Petescia
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and read mapping. Read mapping is a well-studied problem in sequential data, and, together with data structures such as suffix array and Burrows-Wheeler transform, allows for efficient computation. Attempts to achieve comparatively high performance on graphs bring many complications si…