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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

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