PopPUNK databases

Databases come in two flavours: reference only, or all genomes. Some also come with external clusters (noted below) which give compatibility with existing schemes. For larger databases you may wish to download using ftp for enhanced reliability/restarts – replace http:// with ftp:// in the links below and use your favourite client.

Typically, the reference only database will be sufficient for the main use case of assigning new samples to PopPUNK clusters, and updating the database with new clusters which have been found. The reference databases are usually significantly smaller.

For more detailed analyses, you may wish to download the all genomes database. If you wish to run either poppunk-visualise or any subclustering within strains this will require the full database.

In either case only the reference genomes will actually be used for query assignment, which does not change the results but gives a good speed up in program runtime.

See the distributing models documentation page for more details.

We welcome contributions for new species, or expansions of these databases via our github.

SpeciesVersionIsolatesLinksReferencesAllExternal clusters
Acinetobacter baumanniiv18263DownloadDownload
Bordetella pertussisv1339PreprintDownloadDownload
Campylobacter jejuniv140303PortalDownloadDownload
Candida albicansv1Coming soon
Enterococcus faecalisv12026PaperDownloadDownload
Enterococcus faeciumv21658PaperDownloadDownload
Escherichia coliv230138Paper & PortalDownloadDownload
Haemophilus influenzaev22289PaperDownloadDownload
Helicobacter pyloriv12201DownloadDownload
Influenza virusv1Coming soon
Klebsiella pneumoniaev31361PaperDownloadDownload
Legionella pneumophilav13116DownloadDownload
Listeria monocytogenesv240474PortalDownloadDownload
Mycobacterium abscessusv1861PaperDownloadDownloadDCC
Mycobacterium tuberculosisv113170PaperDownloadDownloadLineage
Neisseria gonorrhoeaev18801PaperDownloadDownload
Neisseria meningitidisv133379PaperDownloadDownload
Neisseria meningitidisvCCDC26801DiscussionDownload
Pseudomonas aeruginosav16082PaperDownloadDownload
Saccharomyces cerevisiaev1Coming soon
Salmonella sp.v1335647Coming soon
Staphylococcus aureusv142117PortalDownloadDownload
Stenotrophomonas maltophiliav11210PaperDownloadDownload
Streptococcus agalactiaev118029PaperDownloadDownload
Streptococcus dysgalactiae subspecies equisimilisv21602DownloadDownload
Streptococcus mitisv1322PaperDownload
Streptococcus pneumoniaev442157WebsiteDownloadDownloadGPSC
Streptococcus pyogenesv12084PaperDownloadDownload
Streptococcus suisv12424DownloadDownload