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).

fasta_stripgaps command

Strip gap characters from sequences. Gap characters are dash (-) and dot (.). Input must be in FASTA format. Output is written to a FASTA file given by the -fastaout option.

Example

usearch -fasta_strip_gaps alignment.fa -fastaout seqs.fa