Resources

Sheppard Laboratory GitHub

https://github.com/sheppardlab

Genome databases

Campylobacter BIGSdb server
Multispecies BIGSdb server
Helicobacter BIGSdb server
Staphylococcus BIGSdb server
Staphylococcus BIGSdb server (public)
Aquaculture pathogens BIGSdb server

Intergenic region (IGR) analyses (PIGGY)

Thorpe et al. (2017) multilocus intergenic region (IGR) scheme (S_aureus_Intergenic_PIGGY) for Staphylococcus aureus
Link to the database/scheme

S. epidermidis pGWAS study

Méric, Mageiros et al. (2018) Disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis.
Link to the genome database

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Bayliss et al. (2019) PIRATE (Pangenome Iterative Refinement And Threshold Evaluation) identifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds.
PIRATE is freely available under an GNU GPL 3 open source license from [Github]

Supplementary data

  • Banaszkiewicz et al. (tbc) Publicly accessible genomes of Staphylococcus spp. [BIGSdb] [Figshare]
  • Murray, Pascoe et al. (2017) Genome Biology and Evolution – Publicly accessible genomes of Recombination-mediated host-adaptation by avian Staphylococcus aureus [Link]
  • Meric et al. (2015) Genome Biology and Evolution – Publicly accessible genomes of Staphylococcus aureus and S. epidermidis and corresponding sets of core genes [Link]
  • Supplementary material for Méric et al. (2016) The Lancet Infectious Diseases: E. coli NCTC86 genomic characterisation

Cloud-computing

Sign up to MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB).