USEARCH 11

⛔ = Obsolete/Not recommended

🏆 = Selected topic

Sections

• USEARCH topics

List of all commands

Sequence alignment commands

• See also: Output formats, Accept hit options, Alignment parameters

• allpairs_global Align all pairs in FASTx file using global alignment [link]

  • E.g. usearch -allpairs_global pairs.fasta -alnout results.aln

• allpairs_local Align all pairs in FASTx file using local alignment [link]

  • E.g. usearch -allpairs_local seqs.fasta -alnout results.aln

• pairs_global Align pairs of sequences in FASTx file using global alignment [link]

  • E.g. usearch -pairs_global pairs.fasta -alnout results.aln

• pairs_local Align pairs of sequences in FASTx file using local alignment [link]

  • E.g. usearch -pairs_local pairs.fasta -alnout results.aln

Chimera detection and filtering

• annot Annotate OTU sequences as known (mock or large ref. db.), chimeric etc. [link]
  • E.g. usearch -threads 8 -annot mock_reads.fq -knowndb mock_ref.fa -db silva.udb -tabbedout annot.txt -fastqout annot.fq
• uchime2_ref ⛔ Chimera search using UCHIME2 algorithm [link]
  • Better using unoise3 or cluster_otus
  • E.g. usearch -uchime_ref reads.fasta -db 16s_ref.udb -uchimeout out.txt -strand plus -mode sensitive
  • Read more
• uchime3_denovo ⛔ Chimera search using UCHIME3 de-novo algorithm [link]
  • Better using unoise3 or cluster_otus
  • Read more
• unoise3 🏆 Denoise amplicon reads [link]
  • E.g. usearch -unoise3 uniques.fa -zotus zotus.fa -tabbedout unoise3.txt
  • Read more

Sequence, tree and graph-based clustering

• closed_ref ⛔ Make OTU table using closed-reference clustering [link]
  • Not recommended
• cluster_aggd Cluster distance matrix using agglomerative clustering [link]
  • E.g. usearch -cluster_aggd mx.txt -treeout clusters.tree -clusterout clusters.txt -id 0.80 -linkage min
  • See calc_distmx
• cluster_edges Find connected components of graph (single-linkage clustering) [link]
• cluster_fast 🏆 Cluster sequences using UCLUST [link]
  • usearch -cluster_fast query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc
  • Read more
• cluster_otus 🏆 Cluster sequences using UPARSE [link]
• cluster_smallmem Cluster sequencees using UCLUST [link]
• cluster_tree Construct clusters from tree using distance cutoff [link]

Distance matrices

• calc_distmx Calculate sparse distance matrix [link]
• calc_lcr_probs Calculate Lowest Common Rank probabilities from dist. matrix with taxonomy [link]
• distmx_split_identity Split distance matrix into test/training pair for CVI [link]
• tree2distmx Calculate distance matrix implied by tree [link]

Commands for diversity analysis

• alpha_div Calculate alpha diversity metric(s) from OTU table [link]
• alpha_div_rare Calculate alpha diversity metric(s) from OTU table with rarefaction [link]
• alpha_div_sig Statistical significance of alpha diversity correlation with metadata [link]
• beta_div Calculate beta diversity metric(s) from OTU table [link]

Commands for reads in FASTQ format

• fastq_chars Report frequencies of Q score ASCII characters in FASTQ file [link]
• fastq_eestats Report quality/e.e. per position for reads in FASTQ file [link]
• fastq_eestats2 Report number of reads retained at difference length and e.e. cutoffs [link]
• fastq_filter Filter reads in FASTQ file by e.e. and other criteria [link]
• fastq_join Concatenate forward (R1) and reverse (R2) paired reads [link]
• fastq_mergepairs Assemble (merge) paired reads [options] [description]
• fastq_sra_splitpairs Recover paired reads from SRA interleaved or concatenated format [link]

Commands for sequences in FASTx format (FASTA and FASTQ)

• allpairs_global Align all pairs in FASTx file using global alignment [link]
• allpairs_local Align all pairs in FASTx file using local alignment [link]
• fasta_explode De-unique FASTA file with size=nnn annotations [link]
• fasta_stripgaps Remove gap symbols from FASTA file [link]
• fastx2qiime Convert sample labels from usearch to QIIME format [link]
• fastx_demux Assign reads to samples (demultiplex) [link]
• fastx_findorfs Identify ORFs in nucleotide sequences [link]
• fastx_get_sample_names Extract sample names from FASTx file [link]
• fastx_getlabels Extract sequence labels from FASTx file [link]
• fastx_getseq Extract sequence(s) matching label [link]
• fastx_getseqs Extract sequence(s) matching labels [link]
• fastx_getsubseq Extract subsequence given label, start, stop [link]
• fastx_info Report summary information about a FASTx file [link]
• fastx_learn Estimate error rates from amplicon reads [link]
• fastx_mask Mask low-complexity sequence [link]
• fastx_relabel Re-label sequences in FASTx file with prefix plus sequential number [link]
• fastx_revcomp Reverse-complement nucleotide sequence [link]
• fastx_split Divide sequences in FASTx file into given number of files [link]
• fastx_strip_annots Remove usearch-style annotations (name=xxx) from FASTx file [link]
• fastx_subsample Extract random sub-sample from FASTx file [link]
• fastx_syncpairs Sort forward and reverse reads into the same order [link]
• fastx_trim_primer Remove primer-binding sequence from FASTx file [link]
• fastx_truncate Truncate sequences in FASTx file [link]
• fastx_uniques Identify unique sequences in FASTx file (dereplicate) [link]
• fastx_uniques_persample Identify unique sequences per sample in FASTx file [link]
• filter_lowc Filter low-complexity sequences from FASTx file [link]
• filter_phix Remove PhiX spike sequences from FASTx file [link]
• sortbylength Sort sequences in FASTx file by decreasing length [link]
• sortbysize Sort sequences in FASTx file by decreasing size=nnn [link]

Machine learning and finding informative OTUs

• forest_classify Classify data using random forest [link]
• forest_train Train random forest [link]
• otutab_core Identify core microbiome in OTU table [link]
• otutab_forest_classify Classify samples using random forest [link]
• otutab_forest_train Train random forest on OTU table [link]
• otutab_select Identify OTUs which are informative (predictive of metadata) [link]

Miscellaneous commands

• search_16s Identify 16S sequences in chromosomes or contigs [link]
  • usearch -search_16s contigs.fa -bitvecgg97.bitvec -fastaout 16s.fa
  • See search_16s to prepare the database
• udb2bitvec Create database for search_16s command [link]

Commands for OTU analysis and denoising

• alpha_div Calculate alpha diversity metric(s) from OTU table [link]
• alpha_div_rare Calculate alpha diversity metric(s) from OTU table with rarefaction [link]
• alpha_div_sig Statistical significance of alpha diversity correlation with metadata [link]
• annot Annotate OTU sequences as known (mock or large ref. db.), chimeric etc. [link]
• beta_div Calculate beta diversity metric(s) from OTU table [link]
• closed_ref Make OTU table using closed-reference clustering [link]
• cluster_aggd Cluster distance matrix using agglomerative clustering [link]
• cluster_otus Cluster sequences using UPARSE [link]
• fastx_learn Estimate error rates from amplicon reads [link]
• filter_lowc Filter low-complexity sequences from FASTx file [link]
• filter_phix Remove PhiX spike sequences from FASTx file [link]
• nbc_tax Predict taxonomy using RDP Naive Bayesian Classifier algorithm [link]
• otutab Generate OTU table [link]
• otutab2biom Convert OTU table from tabbed to biom (json) format [link]
• otutab_binary Convert OTU table with counts to presence(1)/absence(0) [link]
• otutab_core Identify core microbiome in OTU table [link]
• otutab_counts2freqs Convert counts to frequencies in OTU table [link]
• otutab_forest_classify Classify samples using random forest [link]
• otutab_forest_train Train random forest on OTU table [link]
• otutab_group Sum subsets of samples in OTU table [link]
• otutab_merge Merge two or more OTU tables [link]
• otutab_octave Generate octave plot visualizing OTU abundance distribution [link]
• otutab_otu_subset Extract subset of OTUs from OTU table [link]
• otutab_otus Extract OTU names from OTU table [link]
• otutab_rare Rarefy OTU table so that samples have same number of reads [link]
• otutab_sample_subset Extract subset of samples from OTU table [link]
• otutab_samples Extract sample names from OTU table [link]
• otutab_select Identify OTUs which are informative (predictive of metadata) [link]
• otutab_sortotus Sort OTU table in order of decreasing OTU size [link]
• otutab_stats Report summary information about OTU table [link]
• otutab_trim Trim OTU table to remove small counts, OTU and/or samples [link]
• otutab_xtalk Estimate and filter cross-talk in OTU table [link]
• qiimemap2otutab Convert QIIME map file to OTU table [link]
• search_oligodb Search for matches to short nucleotide sequences, e.g. primers [link]
• search_pcr In-silico PCR, search for matches to pairs of primers in database [link]
• search_pcr2 In-silico PCR, search for matches to primer pair [link]
• search_phix Search for matches to PhiX sequence [link]
• sinaps Predict traits [link]
• sintax Predict taxonomy using SINTAX algorithm [link]
• sintax_summary Generate summary report from sintax output [link]
• tabbed2otutab Convert read mapping file (read+OTU) to OTU table [link]
• uchime2_ref Chimera search using UCHIME2 algorithm [link]
• uchime3_denovo Chimera search using UCHIME3 de-novo algorithm [link]
• unbias Correct abundance bias in OTU table [link]
• unoise3 Denoise amplicon reads [link]
• uparse_ref Classify sequences derived from mock community sample [link]

OTU table commands

• alpha_div Calculate alpha diversity metric(s) from OTU table [link]
• alpha_div_rare Calculate alpha diversity metric(s) from OTU table with rarefaction [link]
• alpha_div_sig Statistical significance of alpha diversity correlation with metadata [link]
• beta_div Calculate beta diversity metric(s) from OTU table [link]
• otutab Generate OTU table [link]
• otutab2biom Convert OTU table from tabbed to biom (json) format [link]
• otutab_binary Convert OTU table with counts to presence(1)/absence(0) [link]
• otutab_core Identify core microbiome in OTU table [link]
• otutab_counts2freqs Convert counts to frequencies in OTU table [link]
• otutab_forest_classify Classify samples using random forest [link]
• otutab_forest_train Train random forest on OTU table [link]
• otutab_group Sum subsets of samples in OTU table [link]
• otutab_merge Merge two or more OTU tables [link]
• otutab_octave Generate octave plot visualizing OTU abundance distribution [link]
• otutab_otu_subset Extract subset of OTUs from OTU table [link]
• otutab_otus Extract OTU names from OTU table [link]
• otutab_rare Rarefy OTU table so that samples have same number of reads [link]
• otutab_sample_subset Extract subset of samples from OTU table [link]
• otutab_samples Extract sample names from OTU table [link]
• otutab_select Identify OTUs which are informative (predictive of metadata) [link]
• otutab_sortotus Sort OTU table in order of decreasing OTU size [link]
• otutab_stats Report summary information about OTU table [link]
• otutab_trim Trim OTU table to remove small counts, OTU and/or samples [link]
• otutab_xtalk Estimate and filter cross-talk in OTU table [link]
• qiimemap2otutab Convert QIIME map file to OTU table [link]
• tabbed2otutab Convert read mapping file (read+OTU) to OTU table [link]
• unbias Correct abundance bias in OTU table [link]

Next-generation reads

• fastq_chars Report frequencies of Q score ASCII characters in FASTQ file [link]
• fastq_eestats Report quality/e.e. per position for reads in FASTQ file [link]
• fastq_eestats2 Report number of reads retained at difference length and e.e. cutoffs [link]
• fastq_filter Filter reads in FASTQ file by e.e. and other criteria [link]
• fastq_join Concatenate forward (R1) and reverse (R2) paired reads [link]
• fastq_mergepairs Assemble (merge) paired reads [link]
• fastq_sra_splitpairs Recover paired reads from SRA interleaved or concatenated format [link]
• fastx2qiime Convert sample labels from usearch to QIIME format [link]
• fastx_demux Assign reads to samples (demultiplex) [link]
• fastx_findorfs Identify ORFs in nucleotide sequences [link]
• fastx_get_sample_names Extract sample names from FASTx file [link]
• fastx_info Report summary information about a FASTx file [link]
• fastx_learn Estimate error rates from amplicon reads [link]
• fastx_subsample Extract random sub-sample from FASTx file [link]
• fastx_syncpairs Sort forward and reverse reads into the same order [link]
• fastx_trim_primer Remove primer-binding sequence from FASTx file [link]
• fastx_truncate Truncate sequences in FASTx file [link]
• filter_lowc Filter low-complexity sequences from FASTx file [link]
• filter_phix Remove PhiX spike sequences from FASTx file [link]
• search_oligodb Search for matches to short nucleotide sequences, e.g. primers [link]
• search_pcr In-silico PCR, search for matches to pairs of primers in database [link]
• search_pcr2 In-silico PCR, search for matches to primer pair [link]
• search_phix Search for matches to PhiX sequence [link]

Sequence database search

• ⛔ makeudb_sintax Make UDB database file for sintax [link]. See makeudb_usearch instead.
• makeudb_ublast Make UDB database file for ublast [link]
• makeudb_usearch Make UDB database file for usearch_global [link]
• search_exact Search for identical sequences [link]
• search_global Search database using global alignment without speed heuristics [link]
• search_local Search database using locbal alignment without speed heuristics [link]
• search_oligodb Search for matches to short nucleotide sequences, e.g. primers [link]
• search_pcr In-silico PCR, search for matches to pairs of primers in database [link]
• search_pcr2 In-silico PCR, search for matches to primer pair [link]
• search_peptidedb Search for matches to short peptide sequences [link]
• search_phix Search for matches to PhiX sequence [link]
• ublast Fast database search using local alignment (much faster than BLAST) [link]
• usearch_global Fast database search using global alignment [link]
• usearch_local Fast database search using local alignment [link]

Taxonomy commands

• calc_lcr_probs Calculate Lowest Common Rank probabilities from dist. matrix with taxonomy [link]
• makeudb_sintax Make UDB database file for sintax [link]
• nbc_tax Predict taxonomy using RDP Naive Bayesian Classifier algorithm [link]
• sintax Predict taxonomy using SINTAX algorithm [link]
• sintax_summary Generate summary report from sintax output [link]

Tree commands

• calc_distmx Calculate sparse distance matrix [link]
• cluster_tree Construct clusters from tree using distance cutoff [link]
• subtree Extract subtree under given node [link]
• tree2distmx Calculate distance matrix implied by tree [link]
• tree_cvt Convert tree between tabbed and Newick formats [link]
• tree_subset Extract tree for subset of leaves [link]

Labels and annotations

• fastx2qiime Convert sample labels from usearch to QIIME format [link]
• fastx_getlabels Extract sequence labels from FASTx file [link]
• fastx_relabel Re-label sequences in FASTx file with prefix plus sequential number [link]
• fastx_strip_annots Remove usearch-style annotations (name=xxx) from FASTx file [link]
• otutab_otus Extract OTU names from OTU table [link]
• otutab_samples Extract sample names from OTU table [link]