Skip to content

Parsnp

Description

parsnp website

Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees.

Environment Modules

Run module spider parsnp to find out what environment modules are available for this application.

Environment Variables

  • HPC_PARSNP_DIR - installation directory
  • HPC_PARSNP_BIN - executable directory
  • HPC_PARSNP_DOC - documentation directory

Citation

If you publish research that uses parsnp you have to cite it as follows:

Treangen, T. J., Ondov, B. D., Koren, S., & Phillippy, A. M. (2014). Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes. bioRxiv. https://doi.org/10.1101/007351

Categories

biology, phylogenetics