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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.



alignment heuristics

Alignment heuristic parameters control fast but approximate methods for finding the alignment with the highest score. These are distinct from alignment scoring parameters, which determine the score of an alignment. Ideally, changing heuristic parameters would not change the reported alignment (because the best alignment would always be found). By contrast, changing alignment scoring parameters will tend to change the alignment, e.g. increasing gap penalties will reduce the number of gaps.

Full dynamic programming
Heuristics can be disabled entirely by using the -fulldp option, which specifies that full dynamic programming algorithms should be used. These algorithms (Needleman-Wunsch for global alignments and Smith-Waterman for local alignments) are much slower than the heuristic algorithms that USEARCH uses by default, but guarantee to find alignments with the maximum possible score.

Local alignment heuristics

Option Default Description
-xdrop_u 16.0 X-drop for ungapped extension.
-xdrop_g 32.0 X-drop for gapped extension.
-hspw 5 nt, 3 aa Word length for seeding HSPs (ignored by ublast).

Global alignment heuristics

Option Default Description
-xdrop_nw 16.0 X-drop for HSP-finding.
-minhsp 16 Minimum HSP length. This sets an upper limit on the minimum [sic]; USEARCH will automatically reduce this limit for short sequences as needed. The default is 32 in versions through 7.0.1090.
-band 16 Minimum band radius for filling gaps between HSPs. The width of the band is 2 x radius + 1, so default width is 33. Smaller values improve speed. Longer values produce better alignments when there are many non-terminal gaps, especially long gaps, in one sequence relative to the other.
-hspw 5 nt, 3 aa Word length for seeding HSPs.