James Ferguson

Also just a note about your usage of `--slow5_threads 128` It might be helpful to read this document on the thread model design for buttery-eel https://github.com/Psy-Fer/buttery-eel/blob/main/docs/thread_model.md That should help understand...

Hey, Yea I think I need to re-add my skipped read methods. Previously guppy would just power through, but Dorado seems to be somewhat more sensitive to this kind of...

Hey Denis, I have a branch called `skipper` that has the skip logic built into buttery-eel. https://github.com/Psy-Fer/buttery-eel/tree/skipper This will detect when dorado doesn't basecall a read, and just returns the...

Also i have found out why these 3 are not called. Their signal lengths are less than the minimum threshold required by dorado (100). these 3 have a signal length...

TODO: add skip list and update docs to explain what these do. NOTE: Latest dorado-server, 7.4.12 changed the 100 signal limit, though unsure what they did. From their release notes:...

This should now be fixed in https://github.com/Psy-Fer/buttery-eel/releases/tag/v0.5.0 cheers James

Hello. There isn't a --trim_strategy in the python library API, so I think you can parse it along to guppy/dorado. Any argument, like `--use_tcp` that isn't in the buttery-eel cli...

Hey Taek, Yea there are things missing, but that is either because they are not in the library API (supplied by ONT), or are not supported (like alignment while basecalling)....

TODO: Add "common" arguments and some command recipes to the docs to help people get going quicker without entering documentation hell.

Hey, I have yet to try the RNA mods methods. Ice got some m6a data we used to train something else with rna004. I'll give it a go on that...