CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.

Analysis of simulated data finds that high quality assemblies from the strategic K-mer extension for scrupulous assemblies (SKESA) contain sufficient information for accurate, high resolution SNP distance estimation, while assemblies from the St. Petersburg genome assembler (SPAdes) contained more false positives. CSP2 SNP distances for 150 real-world clusters (50 each of <i>E. coli</i>, <i>Listeria monocytogenes</i>, and <i>S. enterica</i>) were highly correlated with those from CSP1 and the National Center for Biotechnology Information (NCBI) Pathogen Detection pipeline (<i>E. coli</i> r >= 0.98; <i>Salmonella</i> r = 0.99, <i>Listeria</i> r = 0.99). This evaluation of CSP2 demonstrates its comparability to accepted methods and validates its use within future traceback and outbreak investigations.