Jump to navigation Jump to search


snp-pipeline website  

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

Environment Modules

Run module spider snp-pipeline to find out what environment modules are available for this application.

System Variables

  • HPC_SNP-PIPELINE_DIR - installation directory
  • HPC_SNP-PIPELINE_BIN - executable directory


If you publish research that uses snp-pipeline you have to cite it as follows:

Davis S, Pettengill JB, Luo Y, Payne J, Shpuntoff A, Rand H, Strain E. (2015) CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20