krona_plots.md

Generating Krona Diagrams

The script krona-from-abundances.py can generate Krona plots from MetaCache abundance results.

1. Query MetaCache datatabase with options -abundances and -abundance-per:

metacache query mydatabase myreads -out classification.txt -abundances abund.txt -abundance-per species

2. Then run the script krona-from-abundances.py on abund.txt:

krona-from-abundances abund.txt

This script

• splits the MetaCache abundance file into two separate files for the original abundance counts and the estimated abundances (here abund_orig.txt and abund_est.txt)
• creates a Krona plot HTML file (here abund_.krona.html) that can be viewed in a web browser