What’s the Answer? (QIIME vs Mothur)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is my favorite kind of question. Trying to assess which tools have which features is sometimes challenging. Documentation varies a lot, and because of the nature of a research project rather than a commercial use, it can be hard to get a comparison of different tools and uses from tool the provider’s sites. Having a place to check with folks in the field who aren’t part of one or another software group really helps.

Question: QIIME vs Mothur : Why use one over the other?

In my own “metagenomic” (amplicon based) analysis, I’ve had a preference for using Mothur. My reasons for it are as follows:

  1. Seems like it does a good job (based on analysis with Mock community)
  2. It has a simple SOP that was straight forward to follow and is published

I am very new to community analysis, so Mothur seemed like an easy first step (and I’ve had good support on the forum..so extra bonus). A long the way I’ve gotten questions about using QIIME. After looking into the differences between the two, I still can’t fully grasp what the major differences between the methods are to motivate one person to prefer one method compared to the other. Does one method make the other obsolete?

I would really appreciate if someone who has worked with either (or both) methods could shed some light on why pick one over the other.


Go check out the ensuing discussion. It’s really helpful.