SNP-Pipeline¶

Description¶

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.

Environment Variables¶

HPC_SNPPIPELINE_DIR - installation directory
HPC_SNPPIPELINE_BIN - executable directory

Citation¶

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 https://doi.org/10.7717/peerj-cs.20

Categories¶

biology, phylogenetics