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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.


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