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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.



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