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).

Masking options

USEARCH provides several methods for masking. Query and database sequences can be masked independently using masking provided by an external program or one of the built-in masking algorithms.

Masking options

Option		Description
-qmask method		Masking method for the query file. Used for database searches and clustering.
-dbmask method		Masking method for the database. Used for makeudb_usearch and makeudb_ublast and when a database is loaded from a FASTA file. Ignored if the database is a UDB file; the desired masking must be applied when the UDB file is created.
-hardmask		Use hard masking (overwrite with N or X). Default is soft masking (upper case is unmasked, lower case is masked)..

Masking methods

Method	Type	Description
fastamino	protein	Unpublished method. Default for proteins.
fastnucleo	nucleotide	Unpublished method. Default for nucleotides.
seg	protein	Seg algorithm as used in BLASTP.
dust	nucleotide	Dust algorithm as used in BLASTN.
none	both	No masking, treat lower case and upper case letters as equivalent. This can be used if the input file has already been hard-masked.
user	both	Assume the input file has already been soft-masked so that lower case letters are masked.