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

ABSTRACT:

Background

Accurate genetic distance estimation from pathogen whole-genome sequence data is critical for public health surveillance, and with respect to food safety it provides crucial information within traceback and outbreak investigations. The computational demands required for contemporary bioinformatics pipelines to extract high resolution single nucleotide polymorphisms (SNPs) grow in parallel with the size of pathogen clusters, where single strains of common pathogens such as Escherichia coli and Salmonella enterica can now contain hundreds or thousands of isolates.

Methods

To facilitate rapid analysis of whole-genome sequencing (WGS) data for large clusters of foodborne bacterial pathogens, we introduce the CFSAN SNP Pipeline 2 (CSP2). CSP2 is a bioinfo

SUBMITTER: Literman R 

PROVIDER: S-EPMC12453658 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature