title: UCHIME improves sensitivity and speed of chimera detection.
abstract: BACKGROUND
  Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
  
  
  RESULTS
  We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
  
  
  BACKGROUND
  robert@drive5.com
  
  
  BACKGROUND
  Source, binaries and data: http://drive5.com/uchime.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Tiburon, CA, USA. robert@drive5.com
authors.forename: Robert C
authors.initials: RC
authors.lastname: Edgar
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jose C
authors.initials: JC
authors.lastname: Clemente
authors.forename: Christopher
authors.initials: C
authors.lastname: Quince
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
mesh_terms: D000465:Algorithms; D016477:Artifacts; D019295:Computational Biology; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software