See also
Quality control
for OTU sequences
A PhiX spike-in is used for Illumina sequencing of amplicon libraries for 16S and other marker genes. Then, PhiX is typically found in around 5% of the raw reads. Often, these are filtered before you see the FASTQ files, but not always, and third-party PhiX filtering software may not be accurate. In usearch, PhiX search is based on the ublast algorithm, and is very sensitive.
The search_phix command can be used for
searching and the filter_phix command can
be used for filtering.