Sept. 2012: otupipe is now considered obsolete

See also
  OTU clustering
  SSU metagenomics

About otupipe
Otupipe is a bash script for OTU clustering based on USEARCH. I now consider otupipe to be obsolete because a simpler and faster pipeline gives equally good results on my benchmark tests. My current preferred pipeline is described in OTU clustering.

The key techniques in otupipe were the use of consensus sequences to reduce sequencing errors, and recentering to find natural centroids. It turns out that these techniques give significant improvements with reads truncated at variable positions, but if global trimming is done as a preprocessing step, then there is no clear advantage.

Old downloads
Links to downloads for the last version (1.1.9) are provided here for reference.
  Source code.
  Manual (PDF).
  Gold database.
  readmap2qiime.py (Python script to convert readmap.uc to QIIME OTU table).