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?

Thank you Olga! Much appreciated.