A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

The PopPIPE (github.com/bacpop/PopPIPE) analysis pipeline can be used to subcluster data, create visualisations and run transmission analyses. Preprint now here: www.biorxiv.org/content/10.1... Including a case study on nosocomial transmission of vancomycin resistant Enterococcus faecium