Script for building a dendrogram for environmental metagenomic samples based on their taxonomic composition.
- Perform taxonomic annotation of each sample with Centrifuge
- Run
centrifuge-kreportto get output taxonomy in kraken-format - Run dendrogram.py to build image with dendrogram
python3 dendrogram.py [-c COUNT] [-o OUTPUT] (-s N [N ...] | -t table)
-c COUNT — Number of most abundant taxons to use (default: all). Names will be shown if count <= 50
-o OUTPUT — File to save dendrogram to (default: dendrogam.png)
-s N [N ...] — files with taxonomy of samples from step 2
-t table — one tabular file with taxonomy of samples
It is recommended to set c parameter less than 100 for better visualisation.
Example of dendrogram of viral communities from various lakes:
Developed by Artem Ivanov at Computer Technologies Lab, ITMO University, Saint-Petersburg, Russia
Should you have any problems or feedback, please send them to [email protected]