Inman JM, Sutton GG, Beck E, Brinkac LM, Clarke TH, Fouts DE
Large-Scale Comparative Analysis of Microbial Pan-genomes using PanOCT.
Bioinformatics (Oxford, England). 2018-08-25;
The JCVI Pan-Genome Pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (Pan-genome Ortholog Clustering Tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes, and generate figures, tables, and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used.