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Centrifuge compatibility #407
Description
Hi there! A couple of questions on this:
- Is centrifuge still supported for use with readfish, like you describe in the publication?
- If so are there any plans to include documentation on this?
- If yes to 1) and no to 2), would you be able to point me in the direction of the bit of the source code that I can look at to work out how to adapt my .toml files?
Thanks! 😄
Activity
github-actions commentedon Oct 8, 2025
Thank you for your issue. Give us a little time to review it.
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mattloose commentedon Oct 29, 2025
Hi,
This is a great question. The centrifuge code still exists in the code as published but has not been actively maintained through the subsequent updates to what is now readfish.
Are you looking to implement this again? One way of doing so would be to write some code that ran the centrifuge analysis and then output a new toml file with the name <existing_toml>.toml_live - readfish automatically picks up and reloads a "live" version of a toml.
Hope this helps. Happy to discuss further.
mattarnoldbio commentedon Oct 29, 2025
Hi Matt,
Thanks for the response. I'll see what i can do with minimap for now and if it seems like there would be an advantage to using centrifuge then I'll look into this in more detail as an option and get back in touch.