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Scoary

Description

scoary website

Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.

Environment Modules

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

Environment Variables

  • HPC_SCOARY_DIR - installation directory
  • HPC_SCOARY_BIN - executable directory

Citation

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

Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 2016;17:238 https://doi.org/10.1186/s13059-016-1108-8

Categories

phylogenetics