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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

filter_phix command

See also
  search_phix
  filter_lowc
  Quality control for OTU sequences

Filter reads for hits to the PhiX genome which is used as a spike in Illumina amplicon sequencing.

Input is a FASTA or FASTQ file. A reverse (R2) read file can be specified using -reverse, in which case a read pair is discarded if the forward (R1) and/or reverse (R2) read has a hit to PhiX. If -reverse is specified, -output2 must be specified for the reverse read output file. Output is written in the same format (FASTA or FASTQ) as the input.

Standard output files are supported for reporting PhiX hits.

Multithreading is supported.

Examples

usearch -filter_phix reads.fq -output filtered_reads.fq -alnout hits.txt

usearch -filter_phix reads_fwd.fq -reverse reads_rev.fq -output fil_fwd.fq -output2 fil_rev.fq