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.

Required Modules

Serial

snp-pipeline

System Variables

HPC_SNP-PIPELINE_DIR - installation directory
HPC_SNP-PIPELINE_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