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).

pcrout file

The pcrout file contains hits generated by the search_pcr command. It is a tabbed text file with the following fields.

Field		Description
1		Query label.
2		Query start position (one-based relative to the start of the plus strand, even if the hit is reverse-complemented).
3		Query end position (one-based relative to the start of the plus strand, even if the hit is reverse-complemented).
4		Query sequence length.
5		Label of first primer.
6		Strand of first primer match.
7		Alignment of first primer in "dot" format. Letters that match the primer are shown as dots, letters indicate query sequence letters that do not match.
8		Label of second primer.
9		Strand of second primer match..
10		Alignment of second primer in "dot" format (see field 7).
11		Amplicon length.
12		Amplicon sequence, i.e. the segment of the query sequence that matches the primer. The letters that match the primers are included.
13		Number of differences with first primer.
14		Number of differences with second primer.

Total differences with both primers.