Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria.

Harry Thorpe, Sion Bayliss, Samuel Sheppard, Edward Feil

Research output: Contribution to journalArticlepeer-review

38 Citations (SciVal)


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 demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

Original languageEnglish
Article numbergiy015
Pages (from-to)1-11
Number of pages11
Issue number4
Early online date4 Mar 2018
Publication statusPublished - 1 Apr 2018


  • DNA, Intergenic
  • Escherichia coli/genetics
  • Genome, Bacterial
  • Genomics/methods
  • Staphylococcus aureus/genetics


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