S. pneumoniae GPSC strain assignment


​PopPUNK is a tool developed by John Lees and team for partitioning species into robust clusters and then assigning novel genomes to those clusters. The Global Pneumococcal Sequencing (GPS) project have used PopPUNK to cluster a globally representative set Streptococcus pneumoniae genomes and made the database available to the community.


PopPUNK uses a K-mer based algorithm to rapidly search a query genome against the reference database. Each cluster is identified by a numerical code, known as the GPSC identifier. For full technical details, please follow the link to their website and documentation.


If you use the results from PopPUNK in a publication, please do cite the original paper: John A Lees et al (2019).
Last modified 1yr ago