User-defined blast directory?

[LovellHAGSC]

Dear Dr. Derelle, Thank you for your work with Broccoli. Quick question, is there support for a user-supplied blast directory, like orthofinder -b? I'd like to port my orthology pipelines to Broccoli and compare with orthofinder, but to do this, I'd need to feed it the identical blast results. Thanks, John

[rderelle]

Dear John,

Short answer: I'm afraid such option isn't available.

Firstly, Broccoli is not compatible with Blast, which has a different cigar output format, and can only be ran with Diamond. Secondly, Broccoli deletes all Diamond output files to save disk-space, and there is no implemented option to restart it with already available Diamond output.

If using Diamond is ok with your task, you would need to modify the script corresponding to step 2 in order to not perform a de-novo Diamond search and instead to use the files present in dir_step2. I could help you with that.

best, Romain

[LovellHAGSC]

Thank you. Yeah, diamond is fine. I'll shoot you an email and we can discuss so that this thread doesn't get crazy. Cheers, John