Uclust and Usearch 5.X has a similar naming convention (no explicit name =
denovo, and reference OTU picking for both has the "reference" in the
name).  The otu_prefix string is set to "" when a reference portion of OTU
picking is done (so OTU IDs have exact match to the reference sequences)
and a "denovo" prefix in other cases to prevent a situation where a numeric
OTU ID might match a reference ID.


On Wed, Apr 10, 2013 at 4:09 PM, Jai Ram Rideout
<notifications@github.com>wrote:

> In qiime/pick_otus.py:
>
> > @@ -1203,8 +1204,219 @@ def __call__(self,
> >
> >          return result
> >
> > +class Usearch61OtuPicker(UclustOtuPickerBase):
>
> May be helpful to rename class to Usearch610DeNovoOtuPicker to match the
> reference-based one, and to be more explicit.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/qiime/pull/848/files#r3743854>
> .
>