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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

All commands (by category)


Sequence alignment commands
  allpairs_global  Align all pairs in FASTx file using global alignment
  allpairs_local  Align all pairs in FASTx file using local alignment
  pairs_global  Align pairs of sequences in FASTx file using global alignment
  pairs_local  Align pairs of sequences in FASTx file using local alignment

Chimera detection and filtering
  annot  Annotate OTU sequences as known (mock or large ref. db.), chimeric etc.
  uchime2_ref  Chimera search using UCHIME2 algorithm
  uchime3_denovo  Chimera search using UCHIME3 de-novo algorithm
  unoise3  Denoise amplicon reads

Sequence, tree and graph-based clustering
  closed_ref  Make OTU table using closed-reference clustering
  cluster_aggd  Cluster distance matrix using agglomerative clustering
  cluster_edges  Find connected components of graph (single-linkage clustering)
  cluster_fast  Cluster sequences using UCLUST
  cluster_otus  Cluster sequences using UPARSE
  cluster_smallmem  Cluster sequencees using UCLUST
  cluster_tree  Construct clusters from tree using distance cutoff

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

Commands for diversity analysis
  alpha_div  Calculate alpha diversity metric(s) from OTU table
  alpha_div_rare  Calculate alpha diversity metric(s) from OTU table with rarefaction
  alpha_div_sig  Statistical significance of alpha diversity correlation with metadata
  beta_div  Calculate beta diversity metric(s) from OTU table

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

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

Machine learning and finding informative OTUs
  forest_classify  Classify data using random forest
  forest_train  Train random forest
  otutab_core  Identify core microbiome in OTU table
  otutab_forest_classify  Classify samples using random forest
  otutab_forest_train  Train random forest on OTU table
  otutab_select  Identify OTUs which are informative (predictive of metadata)

Miscellaneous commands
  search_16s  Identify 16S sequences in chromosomes or contigs
  udb2bitvec  Create database for search_16s command

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

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

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

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

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

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

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