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.