USEARCH manual
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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

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