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).

Merging 2 x 250 reads with long overlap

With very long overlaps such as typical 2 x 250 V4 you will sometimes find that it is better to allow more differences in the alignment; see example report. For example, you might choose to increase set -fastq_maxdiffs 10 -fastq_pctid 80:

usearch -fastq_mergepairs *R1*.fastq -relabel @ -fastq_maxdiffs 10 -fastq_pctid 80 \
-fastqout merged.fq