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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

Paired read assembler comparison


For methods, see Edgar & Flyvbjerg (2015).
Program Mean match
Q error
Mean mismatch
Q error
Random merge
test
BBmerge v8.82 -6.1 -0.5 Pass
COPE v1.1.2 -15.3 13.6
 (25% wrong sign)
Pass
FLASH v1.2.11 -8.8 -0.4 Pass
fastq-join
Download 21 Nov 2015
-8.7 -0.3 Pass
mothur  v.1.36.1
Make.contigs
(Uses PANDAseq method to calculate Qs, but recommends not to use for quality filtering). Fail
(100% assembled)
(May not be a problem if mothur SOPs are followed).
PANDAseq v2.8 -21.6
(73% wrong sign)
-11.6
(20% wrong sign)
Fail
(~70% assembled)
PEAR v0.9.5 -1.3 15.11
(27% wrong sign)
Pass
SeqPrep
Dated 6 Jan 2015
7.3 -0.6 Pass
USEARCH v8.1 fastq_mergepairs 0 0 Pass