pubMLST

Project-specific genome databases

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

Software

https://github.com/sheppardlab

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

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

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

• 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).