Converting fastq to OTU

Hi. I am pretty new to bioinformatics, so please excuse me if this is simple.

I am trying to convert a fastq readings into OTU tables. I assume this is a basic operation, so I thought I might find a simple routine to do this. However, I coudn't find a straightforward way to achieve this in the tutorials nor this forum.

Does someone knows if such a routine exist?

Thanks, Eitan

Hi @eaDumbledore, Welcome to the QIIME 2 Forum!

This isn't a simple conversion, but a process involving quality control and definition of microbiome features (e.g., OTUs, as you mention, but it is much more common to use Amplicon Sequence Variants (ASVs) these days).

You can find this documented in many of our tutorials, including the Moving Pictures tutorial and the Cancer Microbiome Intervention Tutorial (see the "Upstream Tutorial" sections). You can also see this covered in our video courses (the Cancer Microbiome Intervention Tutorial has a corresponding video tutorial here).

Hope this helps - good luck!


Hello Professor,
Thank you
I will certainly follow your instructions!