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).

Compressed alignments

A compressed alignment represents an alignment in a compact format that does not include the sequence letters. The representation uses run-length encoding, as follows. Each column in the alignment is classified as M, D or I.

Column		Description
M		Match. A pair of letters.
D		Delete. A gap in the target.
I		Insert. A gap in the query.

If there are n consecutive columns of type C, this is represented as nC. For example, 123M is 123 consecutive matches. As a special case, if n=1 then n is omitted. So for example, D5M2I3M represents an alignment of this form:

Query XXXXXX--XXX
Target -XXXXXXXXXX