Sardyne: Estimating genome quality using pseudogenes

This is part of the Extremely Open Science Project, where we are developing a tool for genome evaluation in the open. See the project notes for more information.

Getting started

1. Follow the instructions on notes/startup.md to get started.
2. Get the data (data/ subdirectory) by running the download-data.py Jugfile (jug execute download-data.py).
3. Change into the source/ directory and run the simulate.py Jugfile to run the main analysis (jug execute run-sardyne.py). This will take a while.
4. The other files in source/ are exploring the results. This is a WIP.

Joining the project

1. Subscribe on YouTube
2. Join the mailing-list and write in with your thoughts and comments
3. Join the discord server

References

1. Many purported pseudogenes in bacterial genomes are bona fide genes by Cooley & Wright http://dx.doi.org/10.1186/s12864-024-10137-0

License: MIT