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Topics in sequence analysis

OTU analysis
Defining and interpreting OTUs
  Interpreting counts and frequencies in an OTU table
  Read abundances do not correlate with species abundances!
  Mapping reads to OTUs
  Quality control for OTU sequences
  Abundance bias
  Problems with closed- and open-reference OTUs
  Comparing two sets of OTUs for the same reads
  2x250 PE can sequence more than V4
  For best results, pool all samples together
  Critique of Westcott & Schloss 2017 OptiClust paper

Clustering methods
  Greedy clustering
  Agglomerative clustering
  Connected components
  Clustering metagenomics contigs
  Clustering by local alignment
  Defining accuracy for taxonomy classifiers
  Confidence measures for taxonomy predictions


Diversity analysis
  Alpha diversity
  Beta diversity
  Effective number of species

Next-generation reads
Quality filtering
  Expected errors
  Quality (Phred) scores
  Average Q scores are a bad idea
  Should you increase max e.e. for long reads?
  Denoising 454, PacBio and Ion Torrent reads
  Paired-read assembly
  Cross-talk between multiplexed samples

  Defining unique sequence abundance
  Masking low-complexity sequences
  NAST multiple alignments
  PCR amplicon prediction