Is there currently any alternative taxonomic assignment methods with better speed/acc than uclust?

[Jay T]

I'm using a vsearch alias to pick OTUs in the open reference workflow but find that the workflow chokes when it gets to the taxonomic assignment part which I believe is after step 4. Any ideas?

Thanks,

JT

[Colin Brislawn]

Hello JT,

Great question. VSEARCH implements the commands from usearch v7, while qiime makes use of usearch v5, v6.1, and v1.2. So some steps work better than other.

As for taxonomy assignment, you would trying using the RDP classifier, or perhaps the SortMeRNA classifier. There are many methods available in the script, including classics 'like top hit from a BLAST search.' 

http://qiime.org/scripts/assign_taxonomy.html

Let me know if these work well for you,

Colin