CFSAN SNP pipeline

This tutorial demonstrates how to launch the CFSAN SNP pipeline - a pipeline created by the FDA Center for Food Safety and Applied Nutrition (CFSAN)(1) - on sequence read sets in a BIONUMERICS database. 

(1): Steve Davis, James B Pettengill, Yan Luo, Justin Payne, Al Shpuntoff, Hugh Rand, and Errol Strain. Cfsan snp pipeline: an automated method for constructing snp matrices from next-generation sequence data. PeerJ Computer Science, 1:e20, 2015.

wgSNP analysis

Whole-genome Single Nucleotide Polymorphism (SNP) analysis using BIONUMERICS. See the wgSNP application page for a complete overview.
Download PDF file: 
Download demonstration database: 
WGS_demo_database_for_Salmonella_enterica

Demonstration database containing data for a set of 62 Salmonella enterica isolates. This database uses publicly available next-generation sequence reads from the Sequence Read Archive (SRA). For each isolate, NGS reads were de novo assembled into genome sequences. wgMLST alleles were called using the assembly-based and assembly-free method.

Note that the downloaded database backup file (.bnbk) can be restored via the Restore database... functionality in the BIONUMERICS startup screen.