Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies.

ABSTRACT:

Background

A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools.

SUBMITTER: Shapiro JW 

PROVIDER: S-EPMC8351571 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature