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).

search_phix command

See also
filter_phix command

Search sequences for hits to the PhiX genome which is used as a spike in Illumina amplicon sequencing. This command works exactly like ublast except that no database file is needed (no -db option) because the database is compiled into usearch.

Use the filter_phix command to filter paired reads.

Example

usearch -search_phix reads.fq -notmatchedfq filtered_reads.fq -alnout hits.txt