CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. - Steve Davis 002; James B. Pettengill; Yan Luo; Justin Payne; Al Shpuntoff; Hugh Rand; Errol Strain (PeerJ Comput. Sci., 2015)

TreeToReads - a pipeline for simulating raw reads from phylogenies. - Emily Jane McTavish; James B. Pettengill; Steve Davis 002; Hugh Rand; Errol Strain; Marc Allard; Ruth E. Timme (BMC Bioinform., 2017)

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens. - Tim Muruvanda; Hugh Rand; James B. Pettengill; Arthur Pightling (Frontiers Bioinform., 2024)

CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies. - Robert Literman; Jayanthi Gangiredla; Hugh Rand; James B. Pettengill (PeerJ Comput. Sci., 2025)