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Sanger to BLASTn analysis (Read 2806 times)

Sep 29^th, 2019 at 9:13am

bughunter Offline
YaBB Newbies

Posts: 2

Hello,

I use 16S and ITS Sanger sequencing to identify organisms but I can't seem to find/create what I thought would be a pretty simple workflow. I'm not aligning to a known sequence as the entire point is to identify "unknown" organisms. My ideal workflow would be:

Read Sequences > Sequence Quality Trimmer > CAP3 Assembly > BLASTn search

It doesn't seem possible to connect the trim and assembly step, however (the tool for assembly only recognizes output from Read Sequences on my end). Does anyone have suggestions for creating this workflow?

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Reply #1 - Sep 30^th, 2019 at 2:30pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Thank you for your feedback!

Indeed, it's better to modify the CAP3 element, so that it supports the described scenario. I've created an issue about that in out tracker: https://ugene.dev/tracker/browse/UGENE-6607.

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Reply #2 - Sep 30^th, 2019 at 7:00pm

bughunter Offline
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Posts: 2

Thank you Olga! Much appreciated.

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