This is a first pass at doing rRNA read assignment with sortmerna. This code is completely untested, but provides the framework for starting to test this as an alternative to QIIME's existing taxonomy assigners.
To use this code you'll need:
- QIIME 1.8.0 or later
- scikit-bio (latest GitHub version)
- The sortmerna binaries in your
git clone https://gist.github.com/10506167.git smr-tax