UCHIME improves sensitivity and speed of chimera detection

Motivation: 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, causin...

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Bibliographic Details
Published in:Bioinformatics Vol. 27; no. 16; pp. 2194 - 2200
Main Authors: Edgar, Robert C., Haas, Brian J., Clemente, Jose C., Quince, Christopher, Knight, Rob
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 15.08.2011
Subjects:
Algorithms
Biological and medical sciences
Computational Biology
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Original Papers
Polymerase Chain Reaction
Sequence Analysis, DNA - methods
Software
Detection
Sensitivity
Chimera
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary:Motivation: 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. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
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Associate Editor: Martin Bishop
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btr381