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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.



Terminal and internal gaps

See also
Sequence identity

  show_termgaps option

Terminal gaps
A terminal gap is an alignment gap which starts in the first column or ends in the last column. Local alignments never have terminal gaps.

Internal gaps
An internal gap is any gap that is not a terminal gap. Local alignments may have internal gaps.

The global alignment below has terminal and internal gaps indicated. The -show_termgaps option was used for the -alnout output file. Note that the number of columns (302 in this example) is always reported without terminal gaps, as these are the columns used to calculate identity.