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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.



pairs_local command

Aligns pairs of sequences in a FASTA file using local alignment. The first two sequences (1st and 2nd) are aligned, then the second pair (3rd and 4th) and so on up to the N-1th and Nth sequence. To align all-vs.-all, use allpairs_local. Alignments are constructed and reported unconditionally; accept and termination conditions are not supported. More than one alignment may be reported for a given pair. Multithreading is not supported, but this feature could be added.

See also:
  Standard output file options
  Alignment parameters
  Alignment heuristics


usearch -pairs_local pairs.fasta -alnout results.aln