Fig. 1

Overview of typical analysis workflow. Starting with whole genome sequences, the first step is genome annotation, then identification of elements of the pangenome, for which common tools are shown. The main input to the GraPPLE script library is the gene presence/absence matrix (in binary format). From this, pairwise Jaccard similarities are calculated, then converted to a list with annotations (compliant with the “.layout” file schema for Graphia load); as of version 3, Graphia can also load these matrices natively (see Additional file 1: Methods). Suggested filters and transformations to apply within Graphia are listed in order. GraPPLE also contains scripts to change the file formats of synteny graphs produced by common tools (where necessary) to allow for loading into Graphia, again with suggested transformations listed