Basic Use

Contents:

• Downloading Genomes from NCBI
  • Download all genomes in a single taxon
  • Download all genomes from multiple taxa
  • Dry-run test (identify, but do not download, files)
  • Download genomes for compilation of a custom Kraken database
• Indexing Genomes
  • What does indexing do?
  • Index a directory of FASTA files
• Creating a Local pyani Database
  • Create a new empty pyani database
  • Create an empty pyani database at a specific location
• Running ANIm analysis
  • Perform ANIm analysis
  • Perform ANIm analysis with Open Grid Scheduler
  • References
• Interpreting the Graphical Output
  • The Output
  • Heatmaps
  • Distribution Plots
  • Scatterplots
  • Plot Asymmetry