CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.
Year: 2025
Type: article
Abstract: Background: 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 bioinformatics pipeline coded in Nextflow and Python that extracts SNPs directly from genome assemblies in seconds through rapid MUMmer whole-genome alignment and parallel processing. After genome alignment, most data processing steps mirror the quality control measures used in the CFSAN SNP Pipeline (CSP1), including density filtering and missing data handling. Results: r = 0.99). This evaluation of CSP2 demonstrates its comparability to accepted methods and validates its use within future traceback and outbreak investigations.
Source: PubMed
Institution: United States Food and Drug Administration
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4414491322