Fast and compact matching statistics analytics.

ABSTRACT:

Motivation

Fast, lightweight methods for comparing the sequence of ever larger assembled genomes from ever growing databases are increasingly needed in the era of accurate long reads and pan-genome initiatives. Matching statistics is a popular method for computing whole-genome phylogenies and for detecting structural rearrangements between two genomes, since it is amenable to fast implementations that require a minimal setup of data structures. However, current implementations use a single core, take too much memory to represent the result, and do not provide efficient ways to analyze the output in order to explore local similarities between the sequences.

Results

We develop practical tools for computing matching statistics between large-scale strings, and for analyzing its

SUBMITTER: Cunial F 

PROVIDER: S-EPMC9665870 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature