Missing usage option(s)!

[OZTaekOppa]

Thank you for the excellent program. I am currently testing the latest version with several parameters for ONT ultra-long read datasets. However, I noticed a potential omission in usage options and explanations, specifically "--trim_strategy dna." Just to ensure there are no other missing usages, could you please review and address any oversights?

[Psy-Fer]

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 is parsed through to guppy/dorado callers and tried there. If they don't exist there, then there will probably be an error.

I don't know if you have looked at the guppy/dorado CLI, but it's a massive mess.

Anyway, what does the trim_strategy do exactly and how would you use it?

Cheers,
James

[OZTaekOppa]

Hi James,

After discussing with Hasindu and Jill, she mentioned that "in the past, to remove adapters I've used these settings during re-basecalling; --detect_mid_strand_adapter --trim_adapters --detect_adapter --do_read_splitting --trim_strategy dna."

From the buttery-eel -h, I couldn't precisely discern what it meant. However, it seems to pertain to trimming adapter sequences in a DNA sequence. I am currently testing these parameters "--detect_mid_strand_adapter --trim_adapters --detect_adapter --do_read_splitting --trim_strategy dna" with the latest ONT Ultra-Long datasets (NCIG).

So far, the program is running without any issues on gadi.
I am also testing without the option of --trim_strategy dna.

Can you confirm that the latest buttery-eel version has no missing usages/explanations?

Cheers,

Taek

[Psy-Fer]

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). Refer to the guppy_basecaller --help for all possible options.

On this note, I should add some more explanations about some of the "common" arguments that are parsed through to guppy/dorado and not in the buttery-eel CLI. Things like --use_tcp for instance.

It would be good to know the outcome of the trim_strategy on/off differences. What are the other options other than dna ? I imagine there is a default value?

Cheers,
James

[Psy-Fer]

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