Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

Default index parameters

Default values of index parameters are determined from the command name and sequence type (nucleotide or protein). UBLAST parameters apply to the ublast command, USEARCH parameters apply to usearch_ and cluster_ commands.

Parameter	UBLAST protein	USEARCH protein	UBLAST nucleotide	USEARCH nucleotide
-wordlength	(use pattern)	5	8	8
-pattern	10111011	(use kmers)	(use kmers)	(use kmers)
-alpha	(see below)	aa	nt	nt
-dbstep	1	1	1	1
-dbaccel	1.0	1.0	1.0	1.0
-slots	(don't hash)	(don't hash)	(don't hash)	(don't hash)

The default alphabet for protein ublast is A,KR,DENQ,C,G,H,ILVM,FYW,P,ST.