GcoGSA-BA: a global core genome SNP analysis for Bacillus anthracis.

As an issue of biosecurity, it is important to identify the origin of a suspected sample to distinguish whether it originated from the release of a bioterrorism agent or from environmental contamination with a virulent agent. Here we have developed an analytical pipeline that can infer the phylogenetic position of Bacillus cereus group species, including B. anthracis, from next-generation sequencing reads without extensive genomics skills. GcoGSA-BA can also detect the existence of anthrax plasmid pXO1 carrying 3 anthrax toxins (lethal factor, edema factor, and protective antigen). This pipeline can also be used to correctly infer the phylogenetic position and to detect the suspected isolate carrying anthrax toxins among B. cereus group.