Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria
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Abstract
Despite overwhelming evidence that variation in intergenic regions (IGRs) in bacteria impacts on phenotypes, most current approaches for analysing pan-genomes focus exclusively on protein-coding sequences. To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on IGRs. We demonstrate the use of Piggy for pan-genome analyses of Staphylococcus aureus and Escherichia coli using large genome datasets. For S. aureus, we show that highly divergent (“switched”) IGRs are associated with differences in gene expression, and we establish a multi-locus reference database of IGR alleles (igMLST; implemented in BIGSdb). Piggy is available at https://github.com/harry-thorpe/piggy .
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Now published in GigaScience doi: 10.1093/gigascience/giy015
Harry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeSion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner …
Now published in GigaScience doi: 10.1093/gigascience/giy015
Harry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeSion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Edward J. Feil
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy015 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101033 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101034
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