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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.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



File formats

  Commands to convert file formats
  FASTA files
  FASTQ files
  FASTQ file format options
  Phred (Quality) scores in FASTQ files
  Calculating average Phred (Q) scores is a bad idea
  Sequence labels
  Annotations in sequence labels
  Sequence database files
  IUPAC codes for sequence wildcard letters N, X etc.
  Why doesn't USEARCH support gzipped FASTQ files?
  SAM files
  CIGAR strings in SAM files
  USEARCH Database (UDB) files
  Mothur file formats
  QIIME file formats
  OTU table file formats
  NAST multiple alignment files (nastout)
  Newick tree format
  Metadata file