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) |