tsbrowse

Inspect large genetic genealogies (e.g. ARGs) stored in the tskit "succinct tree sequence" format, via a web app. Tsbrowse can scale to ARGs with millions of samples.

Documentation: https://tskit.dev/tsbrowse/docs/stable/ (latest: https://tskit.dev/tsbrowse/docs/latest/)

It is particularly useful to help evaluate ARGs that have been inferred using tools such as tsinfer, sc2ts, Relate, Threads, etc.

Quickstart

Installation

Install from PyPI:

python -m pip install tsbrowse

A tskit tree sequence must first be preprocessed to a .tsbrowse file:

python -m tsbrowse preprocess /path/to/trees-file

This will write a .tsbrowse file that can then be viewed using the web app:

python -m tsbrowse serve /path/to/tsbrowse-file

This command will launch a web server that can be accessed at http://localhost:8080 in a web browser.

To display the genes track use:

python -m tsbrowse serve /path/to/tsbrowse-file --annotations-file genes.csv

(where genes.csv is a semicolon-separated text file containing a header and information about one gene per row in the order: chr;start;end;strand;ensembl ID;gene name)

An example tree sequence file can be found here: example.trees.

Tips

If you are using Windows Subsystem for Linux (WSL) you may need to disable Numba's CUDA support:

NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file

A PNG of a specific page in tsbrowse can be generated using the screenshot command:

python -m tsbrowse screenshot /path/to/tsbrowse-file mutations

Development

Tests are run with pytest:

python -m pytest

To run the UI tests so you can see what the browser is doing use

python -m pytest --headed --slowmo 1000 tests/test_ui.py

playwright codegen is also useful for writing UI test code.

Citing tsbrowse

If you use tsbrowse in your work, please cite this paper