https://github.com/telatin/usearch11_docs
Markdown documentation for USEARCH 11 (see drive5.com for offical docs)
https://github.com/telatin/usearch11_docs
usearch
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Markdown documentation for USEARCH 11 (see drive5.com for offical docs)
- Host: GitHub
- URL: https://github.com/telatin/usearch11_docs
- Owner: telatin
- Created: 2019-07-16T11:23:15.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2019-08-08T10:47:38.000Z (almost 7 years ago)
- Last Synced: 2025-10-30T00:55:17.997Z (9 months ago)
- Topics: usearch
- Language: Perl
- Size: 51.8 KB
- Stars: 1
- Watchers: 0
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# USEARCH 11
:no_entry: = Obsolete/Not recommended
:trophy: = Selected topic
## Sections
- [USEARCH topics](topics.md)
## List of all commands
#### Sequence alignment commands
- See also: [Output formats](https://www.drive5.com/usearch/manual/output_files.html), [Accept hit options](https://www.drive5.com/usearch/manual/accept_options.html), [Alignment parameters](https://www.drive5.com/usearch/manual/aln_params.html)
- **allpairs_global** Align all pairs in FASTx file using global alignment [[link](https://www.drive5.com/usearch/manual/cmd_allpairs_global.html)]
- _E.g._ `usearch -allpairs_global pairs.fasta -alnout results.aln`
- **allpairs_local** Align all pairs in FASTx file using local alignment [[link](https://www.drive5.com/usearch/manual/cmd_allpairs_local.html)]
- _E.g._ `usearch -allpairs_local seqs.fasta -alnout results.aln`
- **pairs_global** Align pairs of sequences in FASTx file using global alignment [[link](https://www.drive5.com/usearch/manual/cmd_pairs_global.html)]
- _E.g._ `usearch -pairs_global pairs.fasta -alnout results.aln`
- **pairs_local** Align pairs of sequences in FASTx file using local alignment [[link](https://www.drive5.com/usearch/manual/cmd_pairs_local.html)]
- _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](https://www.drive5.com/usearch/manual/cmd_annot.html)]
- _E.g._ `usearch -threads 8 -annot mock_reads.fq -knowndb mock_ref.fa -db silva.udb -tabbedout annot.txt -fastqout annot.fq`
- **uchime2_ref** :no_entry: Chimera search using UCHIME2 algorithm [[link](https://www.drive5.com/usearch/manual/cmd_uchime2_ref.html)]
- 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](https://www.drive5.com/usearch/manual/cmd_uchime2_ref.html)
- **uchime3_denovo** :no_entry: Chimera search using UCHIME3 de-novo algorithm [[link](https://www.drive5.com/usearch/manual/cmd_uchime3_denovo.html)]
- Better using _unoise3_ or _cluster\_otus_
- [Read more](https://www.drive5.com/usearch/manual/cmd_uchime3_denovo.html)
- **unoise3** :trophy: Denoise amplicon reads [[link](https://www.drive5.com/usearch/manual/cmd_unoise3.html)]
- _E.g._ `usearch -unoise3 uniques.fa -zotus zotus.fa -tabbedout unoise3.txt`
- [Read more](https://www.drive5.com/usearch/manual/cmd_unoise3.html)
#### Sequence, tree and graph-based clustering
- **closed_ref** :no_entry: Make OTU table using closed-reference clustering [[link](https://www.drive5.com/usearch/manual/cmd_closed_ref.html)]
- Not recommended
- **cluster_aggd** Cluster distance matrix using agglomerative clustering [[link](https://www.drive5.com/usearch/manual/cmd_cluster_aggd.html)]
- _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](https://www.drive5.com/usearch/manual/cmd_cluster_edges.html)]
- **cluster_fast** :trophy: Cluster sequences using UCLUST [[link](https://www.drive5.com/usearch/manual/cmd_cluster_fast.html)]
- `usearch -cluster_fast query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc`
- [Read more](cluster_fast.md)
- **cluster_otus** :trophy: Cluster sequences using UPARSE [[link](https://www.drive5.com/usearch/manual/cmd_cluster_otus.html)]
- **cluster_smallmem** Cluster sequencees using UCLUST [[link](https://www.drive5.com/usearch/manual/cmd_cluster_smallmem.html)]
- **cluster_tree** Construct clusters from tree using distance cutoff [[link](https://www.drive5.com/usearch/manual/cmd_cluster_tree.html)]
#### Distance matrices
- **calc_distmx** Calculate sparse distance matrix [[link](https://www.drive5.com/usearch/manual/cmd_calc_distmx.html)]
- **calc_lcr_probs** Calculate Lowest Common Rank probabilities from dist. matrix with taxonomy [[link](https://www.drive5.com/usearch/manual/cmd_calc_lcr_probs.html)]
- **distmx_split_identity** Split distance matrix into test/training pair for CVI [[link](https://www.drive5.com/usearch/manual/cmd_distmx_split_identity.html)]
- **tree2distmx** Calculate distance matrix implied by tree [[link](https://www.drive5.com/usearch/manual/cmd_tree2distmx.html)]
#### Commands for diversity analysis
- **alpha_div** Calculate alpha diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div.html)]
- **alpha_div_rare** Calculate alpha diversity metric(s) from OTU table with rarefaction [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_rare.html)]
- **alpha_div_sig** Statistical significance of alpha diversity correlation with metadata [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_sig.html)]
- **beta_div** Calculate beta diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_beta_div.html)]
#### Commands for reads in FASTQ format
- **fastq_chars** Report frequencies of Q score ASCII characters in FASTQ file [[link](https://www.drive5.com/usearch/manual/cmd_fastq_chars.html)]
- **fastq_eestats** Report quality/e.e. per position for reads in FASTQ file [[link](https://www.drive5.com/usearch/manual/cmd_fastq_eestats.html)]
- **fastq_eestats2** Report number of reads retained at difference length and e.e. cutoffs [[link](https://www.drive5.com/usearch/manual/cmd_fastq_eestats2.html)]
- **fastq_filter** Filter reads in FASTQ file by e.e. and other criteria [[link](https://www.drive5.com/usearch/manual/cmd_fastq_filter.html)]
- **fastq_join** Concatenate forward (R1) and reverse (R2) paired reads [[link](https://www.drive5.com/usearch/manual/cmd_fastq_join.html)]
- **fastq_mergepairs** Assemble (merge) paired reads [[options](https://www.drive5.com/usearch/manual/merge_options.html)] [[description](https://www.drive5.com/usearch/manual/cmd_fastq_mergepairs.html)]
- **fastq_sra_splitpairs** Recover paired reads from SRA interleaved or concatenated format [[link](https://www.drive5.com/usearch/manual/cmd_fastq_sra_splitpairs.html)]
#### Commands for sequences in FASTx format (FASTA and FASTQ)
- **allpairs_global** Align all pairs in FASTx file using global alignment [[link](https://www.drive5.com/usearch/manual/cmd_allpairs_global.html)]
- **allpairs_local** Align all pairs in FASTx file using local alignment [[link](https://www.drive5.com/usearch/manual/cmd_allpairs_local.html)]
- **fasta_explode** De-unique FASTA file with size=nnn annotations [[link](https://www.drive5.com/usearch/manual/cmd_fasta_explode.html)]
- **fasta_stripgaps** Remove gap symbols from FASTA file [[link](https://www.drive5.com/usearch/manual/cmd_fasta_stripgaps.html)]
- **fastx2qiime** Convert sample labels from usearch to QIIME format [[link](https://www.drive5.com/usearch/manual/cmd_fastx2qiime.html)]
- **fastx_demux** Assign reads to samples (demultiplex) [[link](https://www.drive5.com/usearch/manual/cmd_fastx_demux.html)]
- **fastx_findorfs** Identify ORFs in nucleotide sequences [[link](https://www.drive5.com/usearch/manual/cmd_fastx_findorfs.html)]
- **fastx_get_sample_names** Extract sample names from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_get_sample_names.html)]
- **fastx_getlabels** Extract sequence labels from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_getlabels.html)]
- **fastx_getseq** Extract sequence(s) matching label [[link](https://www.drive5.com/usearch/manual/cmd_fastx_getseq.html)]
- **fastx_getseqs** Extract sequence(s) matching labels [[link](https://www.drive5.com/usearch/manual/cmd_fastx_getseqs.html)]
- **fastx_getsubseq** Extract subsequence given label, start, stop [[link](https://www.drive5.com/usearch/manual/cmd_fastx_getsubseq.html)]
- **fastx_info** Report summary information about a FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_info.html)]
- **fastx_learn** Estimate error rates from amplicon reads [[link](https://www.drive5.com/usearch/manual/cmd_fastx_learn.html)]
- **fastx_mask** Mask low-complexity sequence [[link](https://www.drive5.com/usearch/manual/cmd_fastx_mask.html)]
- **fastx_relabel** Re-label sequences in FASTx file with prefix plus sequential number [[link](https://www.drive5.com/usearch/manual/cmd_fastx_relabel.html)]
- **fastx_revcomp** Reverse-complement nucleotide sequence [[link](https://www.drive5.com/usearch/manual/cmd_fastx_revcomp.html)]
- **fastx_split** Divide sequences in FASTx file into given number of files [[link](https://www.drive5.com/usearch/manual/cmd_fastx_split.html)]
- **fastx_strip_annots** Remove usearch-style annotations (name=xxx) from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_strip_annots.html)]
- **fastx_subsample** Extract random sub-sample from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_subsample.html)]
- **fastx_syncpairs** Sort forward and reverse reads into the same order [[link](https://www.drive5.com/usearch/manual/cmd_fastx_syncpairs.html)]
- **fastx_trim_primer** Remove primer-binding sequence from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_trim_primer.html)]
- **fastx_truncate** Truncate sequences in FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_truncate.html)]
- **fastx_uniques** Identify unique sequences in FASTx file (dereplicate) [[link](https://www.drive5.com/usearch/manual/cmd_fastx_uniques.html)]
- **fastx_uniques_persample** Identify unique sequences per sample in FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_uniques_persample.html)]
- **filter_lowc** Filter low-complexity sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_lowc.html)]
- **filter_phix** Remove PhiX spike sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_phix.html)]
- **sortbylength** Sort sequences in FASTx file by decreasing length [[link](https://www.drive5.com/usearch/manual/cmd_sortbylength.html)]
- **sortbysize** Sort sequences in FASTx file by decreasing size=nnn [[link](https://www.drive5.com/usearch/manual/cmd_sortbysize.html)]
#### Machine learning and finding informative OTUs
- **forest_classify** Classify data using random forest [[link](https://www.drive5.com/usearch/manual/cmd_forest_classify.html)]
- **forest_train** Train random forest [[link](https://www.drive5.com/usearch/manual/cmd_forest_train.html)]
- **otutab_core** Identify core microbiome in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_core.html)]
- **otutab_forest_classify** Classify samples using random forest [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_classify.html)]
- **otutab_forest_train** Train random forest on OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_train.html)]
- **otutab_select** Identify OTUs which are informative (predictive of metadata) [[link](https://www.drive5.com/usearch/manual/cmd_otutab_select.html)]
#### Miscellaneous commands
- **search_16s** Identify 16S sequences in chromosomes or contigs [[link](https://www.drive5.com/usearch/manual/cmd_search_16s.html)]
- `usearch -search_16s contigs.fa -bitvecgg97.bitvec -fastaout 16s.fa`
- See [search_16s](search_16s.md) to prepare the database
- **udb2bitvec** Create database for search_16s command [[link](https://www.drive5.com/usearch/manual/cmd_udb2bitvec.html)]
#### Commands for OTU analysis and denoising
- **alpha_div** Calculate alpha diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div.html)]
- **alpha_div_rare** Calculate alpha diversity metric(s) from OTU table with rarefaction [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_rare.html)]
- **alpha_div_sig** Statistical significance of alpha diversity correlation with metadata [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_sig.html)]
- **annot** Annotate OTU sequences as known (mock or large ref. db.), chimeric etc. [[link](https://www.drive5.com/usearch/manual/cmd_annot.html)]
- **beta_div** Calculate beta diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_beta_div.html)]
- **closed_ref** Make OTU table using closed-reference clustering [[link](https://www.drive5.com/usearch/manual/cmd_closed_ref.html)]
- **cluster_aggd** Cluster distance matrix using agglomerative clustering [[link](https://www.drive5.com/usearch/manual/cmd_cluster_aggd.html)]
- **cluster_otus** Cluster sequences using UPARSE [[link](https://www.drive5.com/usearch/manual/cmd_cluster_otus.html)]
- **fastx_learn** Estimate error rates from amplicon reads [[link](https://www.drive5.com/usearch/manual/cmd_fastx_learn.html)]
- **filter_lowc** Filter low-complexity sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_lowc.html)]
- **filter_phix** Remove PhiX spike sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_phix.html)]
- **nbc_tax** Predict taxonomy using RDP Naive Bayesian Classifier algorithm [[link](https://www.drive5.com/usearch/manual/cmd_nbc_tax.html)]
- **otutab** Generate OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab.html)]
- **otutab2biom** Convert OTU table from tabbed to biom (json) format [[link](https://www.drive5.com/usearch/manual/cmd_otutab2biom.html)]
- **otutab_binary** Convert OTU table with counts to presence(1)/absence(0) [[link](https://www.drive5.com/usearch/manual/cmd_otutab_binary.html)]
- **otutab_core** Identify core microbiome in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_core.html)]
- **otutab_counts2freqs** Convert counts to frequencies in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_counts2freqs.html)]
- **otutab_forest_classify** Classify samples using random forest [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_classify.html)]
- **otutab_forest_train** Train random forest on OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_train.html)]
- **otutab_group** Sum subsets of samples in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_group.html)]
- **otutab_merge** Merge two or more OTU tables [[link](https://www.drive5.com/usearch/manual/cmd_otutab_merge.html)]
- **otutab_octave** Generate octave plot visualizing OTU abundance distribution [[link](https://www.drive5.com/usearch/manual/cmd_otutab_octave.html)]
- **otutab_otu_subset** Extract subset of OTUs from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_otu_subset.html)]
- **otutab_otus** Extract OTU names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_otus.html)]
- **otutab_rare** Rarefy OTU table so that samples have same number of reads [[link](https://www.drive5.com/usearch/manual/cmd_otutab_rare.html)]
- **otutab_sample_subset** Extract subset of samples from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_sample_subset.html)]
- **otutab_samples** Extract sample names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_samples.html)]
- **otutab_select** Identify OTUs which are informative (predictive of metadata) [[link](https://www.drive5.com/usearch/manual/cmd_otutab_select.html)]
- **otutab_sortotus** Sort OTU table in order of decreasing OTU size [[link](https://www.drive5.com/usearch/manual/cmd_otutab_sortotus.html)]
- **otutab_stats** Report summary information about OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_stats.html)]
- **otutab_trim** Trim OTU table to remove small counts, OTU and/or samples [[link](https://www.drive5.com/usearch/manual/cmd_otutab_trim.html)]
- **otutab_xtalk** Estimate and filter cross-talk in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_xtalk.html)]
- **qiimemap2otutab** Convert QIIME map file to OTU table [[link](https://www.drive5.com/usearch/manual/cmd_qiimemap2otutab.html)]
- **search_oligodb** Search for matches to short nucleotide sequences, e.g. primers [[link](https://www.drive5.com/usearch/manual/cmd_search_oligodb.html)]
- **search_pcr** In-silico PCR, search for matches to pairs of primers in database [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr.html)]
- **search_pcr2** In-silico PCR, search for matches to primer pair [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr2.html)]
- **search_phix** Search for matches to PhiX sequence [[link](https://www.drive5.com/usearch/manual/cmd_search_phix.html)]
- **sinaps** Predict traits [[link](https://www.drive5.com/usearch/manual/cmd_sinaps.html)]
- **sintax** Predict taxonomy using SINTAX algorithm [[link](https://www.drive5.com/usearch/manual/cmd_sintax.html)]
- **sintax_summary** Generate summary report from sintax output [[link](https://www.drive5.com/usearch/manual/cmd_sintax_summary.html)]
- **tabbed2otutab** Convert read mapping file (read+OTU) to OTU table [[link](https://www.drive5.com/usearch/manual/cmd_tabbed2otutab.html)]
- **uchime2_ref** Chimera search using UCHIME2 algorithm [[link](https://www.drive5.com/usearch/manual/cmd_uchime2_ref.html)]
- **uchime3_denovo** Chimera search using UCHIME3 de-novo algorithm [[link](https://www.drive5.com/usearch/manual/cmd_uchime3_denovo.html)]
- **unbias** Correct abundance bias in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_unbias.html)]
- **unoise3** Denoise amplicon reads [[link](https://www.drive5.com/usearch/manual/cmd_unoise3.html)]
- **uparse_ref** Classify sequences derived from mock community sample [[link](https://www.drive5.com/usearch/manual/cmd_uparse_ref.html)]
#### OTU table commands
- **alpha_div** Calculate alpha diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div.html)]
- **alpha_div_rare** Calculate alpha diversity metric(s) from OTU table with rarefaction [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_rare.html)]
- **alpha_div_sig** Statistical significance of alpha diversity correlation with metadata [[link](https://www.drive5.com/usearch/manual/cmd_alpha_div_sig.html)]
- **beta_div** Calculate beta diversity metric(s) from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_beta_div.html)]
- **otutab** Generate OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab.html)]
- **otutab2biom** Convert OTU table from tabbed to biom (json) format [[link](https://www.drive5.com/usearch/manual/cmd_otutab2biom.html)]
- **otutab_binary** Convert OTU table with counts to presence(1)/absence(0) [[link](https://www.drive5.com/usearch/manual/cmd_otutab_binary.html)]
- **otutab_core** Identify core microbiome in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_core.html)]
- **otutab_counts2freqs** Convert counts to frequencies in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_counts2freqs.html)]
- **otutab_forest_classify** Classify samples using random forest [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_classify.html)]
- **otutab_forest_train** Train random forest on OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_forest_train.html)]
- **otutab_group** Sum subsets of samples in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_group.html)]
- **otutab_merge** Merge two or more OTU tables [[link](https://www.drive5.com/usearch/manual/cmd_otutab_merge.html)]
- **otutab_octave** Generate octave plot visualizing OTU abundance distribution [[link](https://www.drive5.com/usearch/manual/cmd_otutab_octave.html)]
- **otutab_otu_subset** Extract subset of OTUs from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_otu_subset.html)]
- **otutab_otus** Extract OTU names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_otus.html)]
- **otutab_rare** Rarefy OTU table so that samples have same number of reads [[link](https://www.drive5.com/usearch/manual/cmd_otutab_rare.html)]
- **otutab_sample_subset** Extract subset of samples from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_sample_subset.html)]
- **otutab_samples** Extract sample names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_samples.html)]
- **otutab_select** Identify OTUs which are informative (predictive of metadata) [[link](https://www.drive5.com/usearch/manual/cmd_otutab_select.html)]
- **otutab_sortotus** Sort OTU table in order of decreasing OTU size [[link](https://www.drive5.com/usearch/manual/cmd_otutab_sortotus.html)]
- **otutab_stats** Report summary information about OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_stats.html)]
- **otutab_trim** Trim OTU table to remove small counts, OTU and/or samples [[link](https://www.drive5.com/usearch/manual/cmd_otutab_trim.html)]
- **otutab_xtalk** Estimate and filter cross-talk in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_xtalk.html)]
- **qiimemap2otutab** Convert QIIME map file to OTU table [[link](https://www.drive5.com/usearch/manual/cmd_qiimemap2otutab.html)]
- **tabbed2otutab** Convert read mapping file (read+OTU) to OTU table [[link](https://www.drive5.com/usearch/manual/cmd_tabbed2otutab.html)]
- **unbias** Correct abundance bias in OTU table [[link](https://www.drive5.com/usearch/manual/cmd_unbias.html)]
#### Next-generation reads
- **fastq_chars** Report frequencies of Q score ASCII characters in FASTQ file [[link](https://www.drive5.com/usearch/manual/cmd_fastq_chars.html)]
- **fastq_eestats** Report quality/e.e. per position for reads in FASTQ file [[link](https://www.drive5.com/usearch/manual/cmd_fastq_eestats.html)]
- **fastq_eestats2** Report number of reads retained at difference length and e.e. cutoffs [[link](https://www.drive5.com/usearch/manual/cmd_fastq_eestats2.html)]
- **fastq_filter** Filter reads in FASTQ file by e.e. and other criteria [[link](https://www.drive5.com/usearch/manual/cmd_fastq_filter.html)]
- **fastq_join** Concatenate forward (R1) and reverse (R2) paired reads [[link](https://www.drive5.com/usearch/manual/cmd_fastq_join.html)]
- **fastq_mergepairs** Assemble (merge) paired reads [[link](https://www.drive5.com/usearch/manual/cmd_fastq_mergepairs.html)]
- **fastq_sra_splitpairs** Recover paired reads from SRA interleaved or concatenated format [[link](https://www.drive5.com/usearch/manual/cmd_fastq_sra_splitpairs.html)]
- **fastx2qiime** Convert sample labels from usearch to QIIME format [[link](https://www.drive5.com/usearch/manual/cmd_fastx2qiime.html)]
- **fastx_demux** Assign reads to samples (demultiplex) [[link](https://www.drive5.com/usearch/manual/cmd_fastx_demux.html)]
- **fastx_findorfs** Identify ORFs in nucleotide sequences [[link](https://www.drive5.com/usearch/manual/cmd_fastx_findorfs.html)]
- **fastx_get_sample_names** Extract sample names from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_get_sample_names.html)]
- **fastx_info** Report summary information about a FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_info.html)]
- **fastx_learn** Estimate error rates from amplicon reads [[link](https://www.drive5.com/usearch/manual/cmd_fastx_learn.html)]
- **fastx_subsample** Extract random sub-sample from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_subsample.html)]
- **fastx_syncpairs** Sort forward and reverse reads into the same order [[link](https://www.drive5.com/usearch/manual/cmd_fastx_syncpairs.html)]
- **fastx_trim_primer** Remove primer-binding sequence from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_trim_primer.html)]
- **fastx_truncate** Truncate sequences in FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_truncate.html)]
- **filter_lowc** Filter low-complexity sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_lowc.html)]
- **filter_phix** Remove PhiX spike sequences from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_filter_phix.html)]
- **search_oligodb** Search for matches to short nucleotide sequences, e.g. primers [[link](https://www.drive5.com/usearch/manual/cmd_search_oligodb.html)]
- **search_pcr** In-silico PCR, search for matches to pairs of primers in database [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr.html)]
- **search_pcr2** In-silico PCR, search for matches to primer pair [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr2.html)]
- **search_phix** Search for matches to PhiX sequence [[link](https://www.drive5.com/usearch/manual/cmd_search_phix.html)]
#### Sequence database search
- :no_entry: **makeudb_sintax** Make UDB database file for sintax [[link](https://www.drive5.com/usearch/manual/cmd_makeudb_sintax.html)]. See makeudb_usearch instead.
- **makeudb_ublast** Make UDB database file for ublast [[link](https://www.drive5.com/usearch/manual/cmd_makeudb_ublast.html)]
- **makeudb_usearch** Make UDB database file for usearch_global [[link](https://www.drive5.com/usearch/manual/cmd_makeudb_usearch.html)]
- **search_exact** Search for identical sequences [[link](https://www.drive5.com/usearch/manual/cmd_search_exact.html)]
- **search_global** Search database using global alignment without speed heuristics [[link](https://www.drive5.com/usearch/manual/cmd_search_global.html)]
- **search_local** Search database using locbal alignment without speed heuristics [[link](https://www.drive5.com/usearch/manual/cmd_search_local.html)]
- **search_oligodb** Search for matches to short nucleotide sequences, e.g. primers [[link](https://www.drive5.com/usearch/manual/cmd_search_oligodb.html)]
- **search_pcr** In-silico PCR, search for matches to pairs of primers in database [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr.html)]
- **search_pcr2** In-silico PCR, search for matches to primer pair [[link](https://www.drive5.com/usearch/manual/cmd_search_pcr2.html)]
- **search_peptidedb** Search for matches to short peptide sequences [[link](https://www.drive5.com/usearch/manual/cmd_search_peptidedb.html)]
- **search_phix** Search for matches to PhiX sequence [[link](https://www.drive5.com/usearch/manual/cmd_search_phix.html)]
- **ublast** Fast database search using local alignment (much faster than BLAST) [[link](https://www.drive5.com/usearch/manual/cmd_ublast.html)]
- **usearch_global** Fast database search using global alignment [[link](https://www.drive5.com/usearch/manual/cmd_usearch_global.html)]
- **usearch_local** Fast database search using local alignment [[link](https://www.drive5.com/usearch/manual/cmd_usearch_local.html)]
#### Taxonomy commands
- **calc_lcr_probs** Calculate Lowest Common Rank probabilities from dist. matrix with taxonomy [[link](https://www.drive5.com/usearch/manual/cmd_calc_lcr_probs.html)]
- **makeudb_sintax** Make UDB database file for sintax [[link](https://www.drive5.com/usearch/manual/cmd_makeudb_sintax.html)]
- **nbc_tax** Predict taxonomy using RDP Naive Bayesian Classifier algorithm [[link](https://www.drive5.com/usearch/manual/cmd_nbc_tax.html)]
- **sintax** Predict taxonomy using SINTAX algorithm [[link](https://www.drive5.com/usearch/manual/cmd_sintax.html)]
- **sintax_summary** Generate summary report from sintax output [[link](https://www.drive5.com/usearch/manual/cmd_sintax_summary.html)]
#### Tree commands
- **calc_distmx** Calculate sparse distance matrix [[link](https://www.drive5.com/usearch/manual/cmd_calc_distmx.html)]
- **cluster_tree** Construct clusters from tree using distance cutoff [[link](https://www.drive5.com/usearch/manual/cmd_cluster_tree.html)]
- **subtree** Extract subtree under given node [[link](https://www.drive5.com/usearch/manual/cmd_subtree.html)]
- **tree2distmx** Calculate distance matrix implied by tree [[link](https://www.drive5.com/usearch/manual/cmd_tree2distmx.html)]
- **tree_cvt** Convert tree between tabbed and Newick formats [[link](https://www.drive5.com/usearch/manual/cmd_tree_cvt.html)]
- **tree_subset** Extract tree for subset of leaves [[link](https://www.drive5.com/usearch/manual/cmd_tree_subset.html)]
#### Labels and annotations
- **fastx2qiime** Convert sample labels from usearch to QIIME format [[link](https://www.drive5.com/usearch/manual/cmd_fastx2qiime.html)]
- **fastx_getlabels** Extract sequence labels from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_getlabels.html)]
- **fastx_relabel** Re-label sequences in FASTx file with prefix plus sequential number [[link](https://www.drive5.com/usearch/manual/cmd_fastx_relabel.html)]
- **fastx_strip_annots** Remove usearch-style annotations (name=xxx) from FASTx file [[link](https://www.drive5.com/usearch/manual/cmd_fastx_strip_annots.html)]
- **otutab_otus** Extract OTU names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_otus.html)]
- **otutab_samples** Extract sample names from OTU table [[link](https://www.drive5.com/usearch/manual/cmd_otutab_samples.html)]