Supporting data for ‘Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria’
Dataset type: Genomic, Software
Data released on February 22, 2018
Thorpe HA; Bayliss SC; Sheppard SK; Feil EJ (2018): Supporting data for ‘Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria’ GigaScience Database. http://dx.doi.org/10.5524/100410
Despite overwhelming evidence that variation in intergenic regions (IGRs) in bacteria can directly influence 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 and registered with SciCrunch (RRID: SCR_015941).
Keywords:
Additional details
Read the peer-reviewed publication(s):
(PubMed: 29635296)
Additional information:
https://github.com/harry-thorpe/piggy
Accessions (data referenced by this study):
BioProject:
PRJEB2756
BioProject:
PRJEB8221
GENBANK:
HE681097
GENBANK:
MRSA252
GENBANK:
BX571856
GENBANK:
AP009351
GENBANK:
AM990992
http://datadryad.org/resource/doi:10.5061/dryad.d7d71