What you Trimmomatic or quality control methods of qiime2?

This is my first experience working with qiime and other platforms for quality reads. So,

Which are you experience using DADA2 vs Trimmomatic or Deblur?

What method would you recommend?

Thank you.

Hi @adcerv,

Welcome aboard!

In the tools you listed DADA2 and Deblur are denoisers and ultimately provide you with a feature table similar to what OTU picking methods use to do, albeit at a much higher resolution and completely different approach. A couple of studies you may be interested in that compares these and other denoising methods are here and here. The short of it is that no one method appears to be superior than the other in all instances but certainly all perform better than OTUs.
From my own personal experience, when dealing with shorter reads ex. 80-160 bp Deblur and DADA2 perform very similarly but Deblur is much faster due to its static error model. With longer reads especially, paired-end reads I prefer DADA2 as it retains more of the reads. This may be very specific to my experience and the type of samples I tend to work with (gut/stool tissues) so YMMV.
As for Trimmomatic, as the name suggests, this tool is more for trimming reads and not denoising your reads so can’t really clump them in together.


It was one of my my questions. Thanks for the nice explanation. :rose:

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