Useful scripts for bioinformatics purposes

dendrogram.py

Script for building a dendrogram for environmental metagenomic samples based on their taxonomic composition.

1. Perform taxonomic annotation of each sample with Centrifuge
2. Run centrifuge-kreport to get output taxonomy in kraken-format
3. 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:

Contact

Developed by Artem Ivanov at Computer Technologies Lab, ITMO University, Saint-Petersburg, Russia

Should you have any problems or feedback, please send them to abivanov@itmo.ru