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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
 New in v11 

search_pcr2 command

See also
  PCR amplicon prediction
  search_pcr command

Extract segments between matches to a primer pair. The input file can be in FASTA or FASTQ format. If both strands are searched, the output is oriented to be on the strand matching the pair.

To search for matches to single primers or probes, use search_oligodb.

The -fwdprimer option specifies the forward primer sequence.

The -revprimer option specifies the reverse primer sequence.

Wildcard letters (e.g., N for any letter) are supported in primer sequences.

The -strand option must be specified.

The -maxdiffs option specifies the maximum allowed number of mismatches with a primer. Default 2.

The -minampl option specifies the minimum length of the segment between the primers.

The -maxampl option specifies the maximum length of the segment between the primers.

The -tabbedout option specifies a tabbed text output file giving results for all input sequences.

The -notmatched option specifies a FASTA format file to contain input sequences which did not match.

The -notmatchedfq option specifies a FASTQ format file to contain input sequences which did not match. The input file must be in FASTQ format.

The -fastaout option is a FASTA format file containing segments between the primers.

The -fastaout option is a FASTQ format file containing segments between the primers. The input file must be in FASTQ format.

Example

usearch -search_pcr2 reads.fq -fwdprimer CCGTCAATTCMTTTRAGT \
  -revprimer GGACTACHVGGGTWTCTAAT -minampl 250 -maxampl 350 \
  -strand both -fastaout v5_hits.fa