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All commands
allpairs_global All-vs-all global alignment
allpairs_local All-vs-all local alignment
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
calc_distmx Calculate distance matrix
calc_distmx_smallmem Calculate distance matrix using memory-saving method
closed_ref OTU assignment by database matching
cluster_agg Agglomerative clustering, input is sequences
cluster_aggd Agglomerative clustering, input is distance matrix
cluster_edges Construct connected components from graph edges
cluster_fast Greedy clustering (UCLUST algorithm)
cluster_otus OTU clustering with chimera filtering (UPARSE-OTU algorithm)
cluster_smallmem Greedy clustering (UCLUST algorithm)
derep_fulllength Find unique sequences and abundances (old name for fastx_uniques)
draw_tree Converts tree to human-readable text file
fasta_explode Split FASTA into one file per sequence
fasta_stripgaps Strip gap characters from sequences
fastq_chars Reports frequencies of Phred (Q) scores in FASTQ file
fastq_eestats Expected error distribution in FASTQ file (long report)
fastq_eestats2 Expected error distribution in FASTQ file (short report)
fastq_filter Quality filter FASTQ and/or convert reads to FASTA format.
fastq_join Concatenate forward (R1) and reverse (R2) reads
fastq_mergepairs Merge (assemble) paired reads with overlaps
fastq_sra_splitpairs Recover R1 and R2 reads from SRA interleaved or concatenated format
fastx2qiime Convert sample names to QIIME-compatible format
fastx_demux Assign reads to samples using index reads (demultiplex)
fastx_findorfs Find Open Reading Frames (ORFs) in FASTX file
fastx_getlabels Get labels from FASTA/Q file
fastx_getseq Extract sequence(s) by label from FASTX file
fastx_getseqs Extract sequence(s) by label from FASTX file
fastx_getsubseq Extract subsequence by label and start-stop coordinates from FASTX file
fastx_info Summarize contents of FASTX file
fastx_learn Estimate error rates for amplicon reads
fastx_mask Low-complexity masking
fastx_relabel Re-label FASTA/Q sequences
fastx_revcomp Reverse-complement nucleotide sequences
fastx_split Split FASTX file into two or more roughly equal-size pieces
fastx_strip_annots Strip annotations from labels
fastx_subsample Extract random subset of sequences in a FASTX file
fastx_truncate Truncate sequences
fastx_uniques Find unique sequences and abundances
fastx_uniques_persample Find unique sequences and abundances per sample
filter_phix Filter PhiX sequences
makeudb_sintax Create database index for sintax
makeudb_ublast Create database index for ublast
makeudb_usearch Create database index for usearch_global and uchime
orient Orient nt sequences to the same strand as a database
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
pairs_global Make pair-wise global alignments
pairs_local Make pair-wise local alignments
qiimemap2otutab Convert QIIME map file to classic format
sam_filter Convert SAM alignments to BLAST6 or human-readable format
search_16s Find 16S genes in chromosomes or contigs
search_exact Search for full-length identical database sequences
search_global Search database (global alignments, no index)
search_local Search database (local alignments, no index)
search_oligodb Find matches to short nt sequences e.g. primers
search_pcr Search for amplicons (matches to primer pairs)
search_peptidedb Find matches to short a.a. sequences e.g. peptides
search_phix Screen input for matches to PhiX genome
sinaps Predict attributes (traits) from OTU sequences
sintax Predict taxonomy
sortbylength Sort by decresing sequence length
sortbysize Sort by decresing abundance (size= annotations)
tree2distmx Generate distance matrix from tree
tree_cvt Convert between Newick and tabbed formats
ublast Fast database search (local alignment similar to BLAST)
uchime2_ref Find chimeras by database search
uchime3_denovo Filter chimeras in denoised amplicon sequences
udb2bitvec Create bit vector index for search_16s
udb2fasta Extract sequences from UDB file
udbinfo Report index parameters used to make UDB file
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)
usearch_global Fast database search (indexed, global alignment)
usearch_local Fast database search (indexed, local alignment)