Accurate and fast graph-based pangenome annotation and clustering with ggCaller.

ABSTRACT: Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated, and clustered, representing the "pangenome." Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing

SUBMITTER: Horsfield ST 

PROVIDER: S-EPMC10620059 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature