Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria.

ABSTRACT:

Background

The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences.

Findings

To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonst

SUBMITTER: Thorpe HA 

PROVIDER: S-EPMC5890482 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature