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Published 20 hours ago • verified publisher icon jenniferlu717

Protein translated search

Open sschmeier opened this issue 6 years ago • 3 comments

Hi there,

I was wondering if one can use Bracken with a Kraken2 protein database? I have not been able to create a Bracken db with protein sequences.

Cheers, Seb

sschmeier avatar Dec 10 '18 19:12 sschmeier

Currently no, but I'm working on adding in that functionality.

The issue is that now we have to take into consideration every possible DNA sequence that can be translated into the protein sequences in the database, which adds a level of complexity that I need to write a new script for.

I'll update with a new version hopefully within the next month to allow for translated search with Bracken.

jenniferlu717 avatar Dec 13 '18 06:12 jenniferlu717

Hi, just curious if there are any updates on this? Thanks!

cm0109 avatar Jul 18 '20 20:07 cm0109

Hi @jenniferlu717 I am testing a two-step kraken search (nt search, then translated on unclassified reads from nt search), then combining these reports. Do you see a problem with running Bracken on the combined report? Or would it be better to run bracken on the nt search results, then combine the resulting report with the protein search?

Would love to have your thoughts on this. Cheers

jorondo1 avatar Mar 23 '22 18:03 jorondo1