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OTU analysis
See also
OTU / denoising analysis
  Quality control for OTUs 
alpha_div Calculate alpha diversity metrics
alpha_div_rare Calculate alpha diversity metrics with rarefaction (subsampling)
annot Annotate sequences as known, contaminant or chimeric
beta_div Calculate beta diversity metrics
closed_ref OTU assignment by database matching
cluster_otus OTU clustering with chimera filtering (UPARSE-OTU algorithm)
otutab Create OTU table
otutab2biom Convert tabbed-text OTU table to BIOM v1 format
otutab_counts2freqs Convert OTU table from counts to frequencies.
otutab_freqs2counts Convert OTU table from frequencies to counts
otutab_group Combine samples into groups
otutab_merge Merge two or more OTU tables
otutab_norm Normalize OTU table counts to same number of reads per sample
otutab_otu_subset Extract subset of OTUs
otutab_sample_subset Extract subset of samples
otutab_sortotus Sort OTUs by decreasing frequency
otutab_stats Report summary statistics for OTU table
otutab_subsample Subsample (rarefy) OTU table
otutab_trim Delete low-abundance counts, samples and OTUs
qiimemap2otutab Convert QIIME map file to classic format
search_phix Screen input for matches to PhiX genome
sinaps Predict attributes (traits) from OTU sequences
uchime2_ref Find chimeras by database search
uchime3_denovo Filter chimeras in denoised amplicon sequences
unbias Correct for abundance bias in OTU table
uncross Detect cross-talk from OTU table
unoise3 Correct errors (denoise) amplicon reads, includes chimera filter
uparse_ref Classify mock community sequences (recognizes chimeras and read errors)