Pathogen informatics and modelling
graph-gene Caller (ggCaller), combines gene annotation and pangenome clustering steps within population-wide de Bruijn Graphs.
Split k-mer analysis (SKA) can be used to produce alignments from closely related sequence assemblies or reads, quickly (because it is alignment-free) and with minimal fuss (due to the interface).
Calculate core and accessory distances, cluster genomes, assign new genomes to clusters, make visualisations
Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
Search for bacterial genomes and metadata