| 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) |