search_phix command
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



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