The JCVI Pan-Genome Pipeline is a collection of programs designed to allow users to run PanOCT along with numerous other tools that support and extend the capabilities of PanOCT. PanOCT, or Pan-genome Ortholog Clustering Tool, was created as a tool for pan-genomic analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline consists of a series of command-line utilities, invoked by a single wrapper, that: prepare input for analysis, invoke third-party analysis tools such as NCBI Blast+, run PanOCT, annotate features of the resulting pan-genome, detect sets of genes of interest such as AMR genes, and generate figures and tables to visualize the results of the analysis. The pipeline is capable of running in a hierarchical mode, lowering the RAM used by the pipeline, by analyzing subdivisions of the input before running a final PanOCT run that incorporates the results in those subdivisions.

1. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Fouts DE, Brinkac L, Beck E, Inman J, Sutton G. http://www.ncbi.nlm.nih.gov/pubmed/22904089