What you think usearch does might not be what it does

2016/01/05

One day in Athens, the microbiome scientist Everymeno encounters 16Socrates.

Everymeno: Hail, 16Socrates! I’ve been troubled by some results from my 16S amplicon sequencing data, and I was hoping to hear your wisdom.

16Socrates: I don’t know that I can answer your questions, but we can look for an answer together.

E: In a microbiome experiment, I collected samples, extracted the DNA, and amplified the 16S gene. I’m converting the raw 16S sequences into operational taxonomic units (OTUs). I know there’s a lot of discussion in the Microbiome Agora about what kinds of OTU-calling methods we should use, so I tried to avoid controversy by using all of them and seeing what comes out…

The remainder of this dialogue is available at microbe.mit.edu.