Scoary2 associates orthogenes (e.g. generated using OrthoFinder or Roary to traits. It reports a list of genes sorted by strength of association per trait. The results can be explored interactively with a simple, static HTML/JS app.

Wiki

• Home
• Installation
• Usage
• Input
• Output
• Tutorial
• App
• Understanding the p values
• Usage as Python library

Paper

Please cite:

Roder, T. et al. Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes. Genome Biol 25, 93 (2024). https://doi.org/10.1186/s13059-024-03233-7