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USEARCH commands
allpairs_global Compare all pairs of input sequences (global alignment).
allpairs_local Compare all pairs of input sequences (local alignment).
calc_distmx Calculate sparse distance matrix from sequences in FASTA file.
cluster_agg Agglomerative clustering of sequences.
cluster_aggd Agglomerative clustering using distance matrix.
cluster_edges Single-linkage clustering from graph edges in tabbed text file.
cluster_fast Cluster sequences, optimized for speed.
cluster_otus OTU clustering (UPARSE algorithm).
cluster_smallmem Cluster sequences, optimized for low memory use.
depoly Collapse long homopolymers.
derep_fulllength Dereplicate full-length sequences (find uniques).
derep_prefix Dereplicate (find uniques), allowing prefix matches.
distmx2taxprobs Create taxprobs file for utax.
draw_tree Make text "picture" from a tree in Phylip format.
fasta_diversity Report alpha diversity indexes and estimators.
fasta_rarify Calculate rarefaction curve from sequences in FASTA file.
fastq_chars Report statistics Q score ASCII characters in FASTQ file.
fastq_eestats Report expected-error statistics for FASTQ reads.
fastq_filter Quality filter FASTQ reads and/or convert to FASTA.
fastq_join Combine paired reads as R1-NNNNNN-RevComp(R2).
fastq_mergepairs Merge overlapping read pairs into single sequences ("contigs").
fastq_stats Report statistics for FASTQ reads.
fastx_findorfs Find Open Reading Frames (ORFs) in FASTA or FASTQ file.
fastx_getseq Extract sequence with a given label from FASTA file.
fastx_getseqs Extract sequences from FASTA file.
fastx_getsubseq Extract subsequence.
fastx_mask Mask low-complexity regions in FASTA or FASTQ file.
fastx_revcomp Reverse complement sequences.
fastx_split Split FASTA or FASTQ file into approximately equal pieces.
fastx_subsample Generate a random subset of a FASTA or FASTQ file.
fastx_truncate Truncate FASTA or FASTQ sequences at fixed length.
makeudb_ublast Create database index for ublast command.
makeudb_usearch Create database index for usearch_global/local commands.
pairs_global Compare consecutive pairs of input sequences (global alignment).
pairs_local Compare consecutive pairs of input sequences (local alignment).
sam_filter Filter/convert SAM records.
search_exact Database search for 100% identical matches.
search_global Database search, global alignments.
search_local Database search (slow but thorough), local alignments.
search_oligodb Database search, database contains short nt. fragments.
search_pcr Find segments (predicted amplicons) matching a primer pair.
search_peptidedb Database search, database contains short a.a. fragments.
sortbylength Sort sequences by length.
sortbysize Sort sequences by abundance given as "size=N;" field in label.
tree2clusters Agglomerative clustering from a tree in Phylip format.
tree2distmx Calculate distance matrix from a tree in Phylip format.
ublast Database search, local alignments.
uchime_denovo Find chimeric sequences de novo (without ref db).
uchime_ref Find chimeric sequences using reference database.
udb2fasta Extract sequences from database index in FASTA format.
udbinfo Show parameters of database index file.
udbstats Report statistics for database index file.
uparse_ref Classify amplicon sequences using reference database.
usearch_global Database search, global alignments.
usearch_local Database search, local alignments.
utax Taxonomy assignment