title: Comparing clustering and pre-processing in taxonomy analysis.
abstract: BACKGROUND
  Massively parallel sequencing allows for rapid sequencing of large numbers of sequences in just a single run. Thus, 16S ribosomal RNA (rRNA) amplicon sequencing of complex microbial communities has become possible. The sequenced 16S rRNA fragments (reads) are clustered into operational taxonomic units and taxonomic categories are assigned. Recent reports suggest that data pre-processing should be performed before clustering. We assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data.
  
  
  RESULTS
  The number of clusters varied up to two orders of magnitude depending on pre-processing. Pre-processing using both denoising and chimera checking resulted in a number of clusters that was closest to the number of species in the mock dataset (25 versus 15). Based on run time, purity and normalized mutual information, we could not identify a single best clustering algorithm. The differences in clustering accuracy among the algorithms after the same pre-processing were minor compared with the differences in accuracy among different pre-processing steps.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
  
  
  BACKGROUND
  bonder.m.j@gmail.com or b.brandt@acta.nl
authors.affiliation: Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam-ACTA, University of Amsterdam and VU University Amsterdam, VU University Amsterdam, The Netherlands. bonder.m.j@gmail.com
authors.forename: Marc J
authors.initials: MJ
authors.lastname: Bonder
authors.forename: Sanne
authors.initials: S
authors.lastname: Abeln
authors.forename: Egija
authors.initials: E
authors.lastname: Zaura
authors.forename: Bernd W
authors.initials: BW
authors.lastname: Brandt
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000379:methods; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012463:Saliva / Q000737:chemistry
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S