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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.



USEARCH algorithms

 See also
  Papers and citing USEARCH

Algorithm   Description
USEARCH   Ultra-fast global alignment search for high-identity top hit or hits.
UCLUST   Ultra-fast general-purpose clustering. See also OTU clustering.
UBLAST   Fast, sensitive database search by local alignment. Similar to BLAST in some ways, but much faster due to the use of an index.
UPARSE-REF   Error inference by maximum parsimony. Used for annotating sequences obtained in mock community experiments.
UPARSE-OTU   OTU clustering of marker gene reads, e.g. 16S or ITS..
UCHIME2   Search for chimeric sequences.
Dereplication   Find unique sequences (delete duplicated sequences).
ORF detection   Identification of Open Reading Frames (ORFs) in nucleotide sequences.
Local clustering   Clustering using local alignments
Paired read merging   Merging (assembly) of paired reads.
UNOISE2   Error-correction (denoising) of amplicon reads
UTAX   Taxonomy prediction for marker genes (16S, ITS...). Obsolete.
SINTAX   Taxonomy prediction for marker genes (16S, ITS...).
Read quality filtering   Quality filtering of reads with Phred (quality) scores..
Masking   Detection of repetitive or low-complexity regions.
Demultiplexing   Assign reads to samples using index reads.
UNCROSS   Detect and filter cross-talk in a OTU table.
UNBIAS   Correct for amplification bias in an OTU table.