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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