See also: Algorithms.

SEARCH_16S algorithm
Edgar, R.C. (2017), SEARCH_16S: A new algorithm for identifying 16S ribosomal RNA genes in contigs and chromosomes. http://biorxiv.org/content/early/2017/04/04/124131

UNBIAS algorithm
UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success. http://biorxiv.org/content/early/2017/04/04/124149

SINAPS algorithm
SINAPS: Prediction of microbial traits from marker gene sequences. http://biorxiv.org/content/early/2017/04/04/124156

UNCROSS algorithm
Edgar, R.C. (2016), UNCROSS: Filtering of high-frequency cross-talk in 16S amplicon reads. doi: http://dx.doi.org/10.1101/088666

UNOISE algorithm
Edgar, R.C. (2016), UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon reads.http://dx.doi.org/10.1101/081257

SINTAX algorithm
Edgar, R.C. (2016), SINTAX, a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, http://dx.doi.org/10.1101/074161.

UCHIME2 algorithm
Edgar, R.C. (2016), UCHIME2: Improved chimera detection for amplicon sequences, http://dx.doi.org/10.1101/074252.

Expected error filtering and paired read merging
Edgar, R.C. and Flyvbjerg, H (2014) Error filtering, pair assembly and error correction for next-generation sequencing reads
  [doi: 10.1093/bioinformatics/btv401].

UPARSE algorithm
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772,  dx.doi.org/10.1038/nmeth.2604].

USEARCH and UCLUST algorithms
Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.
doi: 10.1093/bioinformatics/btq461

UCHIME algorithm
Edgar,RC, Haas,BJ, Clemente,JC, Quince,C, Knight,R (2011) UCHIME improves sensitivity and speed of chimera detection, Bioinformatics doi: 10.1093/bioinformatics/btr381 [Pubmed 21700674].

UBLAST algorithm
Edgar, RC (unpublished) /usearch