Commands > Search, OTU analysis
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
usearch -search_phix reads.fq -notmatchedfq filtered_reads.fq -alnout