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Data released on February 22, 2018

Supporting data for ‘Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria’

Thorpe, H, A; Bayliss, S, C; Sheppard, S, K; Feil, E, J (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 RIS BibTeX Text

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).

Contact Submitter

Additional information:

https://github.com/harry-thorpe/piggy

Accessions (data not in GigaDB):

BioProject: PRJEB2756
BioProject: PRJEB8221
GENBANK: HE681097
GENBANK: MRSA252
GENBANK: BX571856
GENBANK: AP009351
GENBANK: AM990992
http://datadryad.org/resource/doi:10.5061/dryad.d7d71

Keywords:

pan-genome accessory genome genomics whole-genome sequencing (wgs) bacteria intergenic regions igmlst gene expression staphylococcus aureus escherichia coli 

Software, Genomic

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Funding:

  • Funding body - Medical Research Council
  • Award ID - G1000803
  • Comment - United Kingdom Clinical Research Collaboration Translational Infection Research Initiative
  • Awardee - S Peacock

Files: (FTP site) Table Settings

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File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive3.78 MB2018-02-01
ReadmeTEXT1.41 KB2018-02-01
Displaying 1-2 of 2 File(s).

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