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If you are going to campaign for mothur or QIIME, do your best to accurately represent the strengths of your pet package.When I teach workshops or field users’ questions, I am often asked what I think of QIIME.Certainly, a lot of the functionality within QIIME is written by the QIIME developers, but much of the heavy lifting (e.g.OTU clustering, classification) is from code written by others.As you might expect, the advantage of this approach is that if the developers can write a light wrapper for a new package in Python, then it is pretty painless to bring in other people’s software.Of course, that software comes in warts and all and creates dependency hell.
Sadly, this isn’t the only example of this that I have seen. I’ve looked over their SOPs, talked with a number of QIIME users, and feel that I generally have a good sense of what their strategy is about. QIIME debate (note: the title of this post is mothur and QIIME), but if I misrepresent something or am being unfair, please let me know and I’ll edit this post.Often times the person asking the question or making the dogmatic statement doesn’t seem to have a full appreciation for the differences and similarities and whether the differences are really meaningful.