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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

Default index parameters

 
Default values of index parameters are determined from the command name and sequence type (nucleotide or protein). UBLAST parameters apply to the ublast command, USEARCH parameters apply to usearch_ and cluster_ commands.
 
Parameter UBLAST
protein
USEARCH
protein
UBLAST
nucleotide
USEARCH
nucleotide
-wordlength (use pattern) 5 8 8
-pattern 10111011 (use kmers) (use kmers) (use kmers)
-alpha (see below) aa nt nt
-dbstep 1 1 1 1
-dbaccel 1.0 1.0 1.0 1.0
-slots (don't hash) (don't hash) (don't hash) (don't hash)

 The default alphabet for protein ublast is A,KR,DENQ,C,G,H,ILVM,FYW,P,ST.