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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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Short Sequences #36

Closed antixz1 closed 5 months ago

antixz1 commented 2 years ago

Is there a reason Phigaro dismisses contigs <20000 bp? Is there any way to alter the threshold?

PollyTikhonova commented 2 years ago

Hi, I am so sorry I was sure I addressed the question, but it seems it happened only in my head Yes, there is a technical limitation - Prodigal, which is used for sequence annotation do not process sequences shorter this length. But speaking about the opportunity of allowing Phigaro to run such short sequences, my colleague and I concluded that Phigaro, probably would make no sense at this mode, because the sequence is too short to identify several viral items. Anyway, I am citing here my previous comment to the same question with the algorithm, which would allow you manually to extract the virality of your sequence using Phigaro: https://github.com/bobeobibo/phigaro/issues/31 Hope, it's helpful!