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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.



Unbias reference databases

See also
  UNBIAS algorithm
  unbias command

unbias_dbs_v10.0.tar.gz (4.3 Mb)

Copy number reference (copynr.fa)
Contains full-length 16S sequences. A typical label is:

>U28;copynr=3;sp=Campylobacter coli;

The annotation format should be self-explanatory. This database was created by downloading all finished microbial genomes from Genbank and predicting 16S genes using the search_16s command. For each genome, the number of 16S genes was counted.

V4 primer mismatch database (v4diffs.fa)
Contains V4 sequences. A typical label is:

>U118;v4diffs=0;sp=Bacillus cereus;

The v4diffs annotation gives the total number of mismatches with V4F (GTGCCAGCMGCCGCGGTAA) and V4R (GGACTACHVGGGTWTCTAAT). Mismatches were measured using the search_pcr command. If you need reference data for a different primer pair, let me know.

The unbias reference databases were created by Robert C. Edgar and are licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.

Creative Commons License