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 300 reads with short overlap

Default options for fastq_mergepairs typically work well for this case. Sometimes the R2 quality is bad; see Strategies for dealing with low-quality reverse reads (R2s). Example command-line:

usearch -fastq_mergepairs *R1*.fastq -sample @ -fastqout merged.fq