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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_oligodb command

Search for matches of nucleotide sequences to a database containing short nucleotide sequences (oligonucleotides). The most common use for this command is searching for matches to primers or probes in genome sequences or gene databases.

Wildcard letters indicating degenerate positions in the primer are supported. See IUPAC codes for details.

The algorithm uses a fast and exact method; there are no heuristics, so all matches meeting the accept criteria are guaranteed to be found. Alignments are global; all letters of the database sequence must be aligned to a letter in the query sequence. Gaps are not permitted, except for terminal gaps in the query sequence.

Note that it is the longer sequence (genome, chromosome, gene etc.) that is the query; the database contains the oligos. The name of the command (search_oligodb) is intended to remind you of this, just in case you're used to doing it the other way around, as with some other local aligners like BLAST.

Termination options are supported. By default, termination is disabled, equivalent to -maxaccepts 0 -maxrejects 0. In other words, by default the entire database is searched.

Accept options are supported. By default, -maxdiffs 2 is assumed and other accept criteria are not used.

The query file may be in FASTA or FASTQ format.

A database file must be specified using the -db option and must be in FASTA format.

The -strand option is required for nucleotide databases.

Multithreading is supported.

Standard output files are supported.

usearch -search_oligodb human_genome.fa -db probes.fa -strand both \
  -userout out.txt -userfields query+target+qstrand+diffs+tlo+thi+trowdots