Contains a Jupyter notebook demonstrating how to compare kraken reports across multiple samples for a specified taxonomic rank. The analysis demonstrates how to:
- Generate and save a combined taxon count table for a particular taxonomic rank.
- Create and save stacked barplots showing relative or absolute abundances of taxa across samples.
- NEW: Create and save heatmaps showing relative abundances of taxa across samples.
- Perform analyses at different taxonomic ranks (strains, species, genera, families, etc.)
- NEW: Plot the percentage of reads assigned across taxonomic ranks.
- NEW: Plot the number of unique taxa assigned across taxonomic ranks.
To see the completed analysis, you can click and view the Compare-kreport-taxonomic-profiles.html file, or download and open the Compare-kreport-taxonomic-profiles.html file with a web browser.
Compare-kreport-taxonomic-profiles.html: An html version of the Jupyter notebook, which shows step-by-step results. To see the rendered version, click here.Compare-kreport-taxonomic-profiles.ipynb: A clean version of the above notebook that can be downloaded and used for your own analysis.inputs/: Contains the four kreport files needed to reproduce the analysis.outputs/: Contains the output tables and figures generated by the analysis.
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