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OTUs from multiple marker gene regions

See also
Taxonomy benchmark home
  Greengenes fragment test
  Greengenes fragment test results
  HMP sample test
  HMP sample test results

Can we make OTUs from different regions?
Microbial metagenomics experiments use next-generating sequencing to capture fragments of marker genes such as 16S or ITS. Different experiments often use PCR primers that target different segments of the gene which may not overlap, e.g. the Human Microbiome Project sequenced three different regions: V1-V3, V3-V5 and V6-V9. It would be useful to combine and compare data from different experiments.

Algorithms for making OTUs from different regions
The cluster_otus_utax command uses the UTAX algorithm to create OTUs from predicted taxonomies. This command is very effective at identifying equivalent regions (see tests below). The QIIME closed-ref OTU picking strategy also claims to do this, but my tests show that the performance is very poor -- only a small fraction of equivalent segments are identified.

Testing OTUs from different regions
I designed two tests for this problem: the
Greengenes fragment test and the HMP sample test. For results, see Greengenes fragment test results and HMP sample test results.