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