CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets.

ABSTRACT: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than othe

SUBMITTER: Harris CD 

PROVIDER: S-EPMC7826169 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature