PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.

ABSTRACT:

Background

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.

Results

Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software deve

SUBMITTER: Bayliss SC 

PROVIDER: S-EPMC6785682 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature