SCARAP: scalable cross-species comparative genomics of prokaryotes.

ABSTRACT:

Motivation

Much of prokaryotic comparative genomics currently relies on two critical computational tasks: pangenome inference and core genome inference. Pangenome inference involves clustering genes from a set of genomes into gene families, enabling genome-wide association studies and evolutionary history analysis. The core genome represents gene families present in nearly all genomes and is required to infer a high-quality phylogeny. For species-level datasets, fast pangenome inference tools have been developed. However, tools applicable to more diverse datasets are currently slow and scale poorly.

Results

Here, we introduce SCARAP, a program containing three modules for comparative genomics analyses: a fast and scalable pangenome inference module, a direct core genome infe

SUBMITTER: Wittouck S 

PROVIDER: S-EPMC11681940 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature