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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Veröffentlicht in:	Bioinformatics Jg. 27; H. 16; S. 2194 - 2200
Hauptverfasser:	Edgar, Robert C., Haas, Brian J., Clemente, Jose C., Quince, Christopher, Knight, Rob
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Oxford Oxford University Press 15.08.2011
Schlagworte:	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-Zugang:	Volltext
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Zusammenfassung:	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.
Bibliographie:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 Associate Editor: Martin Bishop
ISSN:	1367-4803 1367-4811 1460-2059 1367-4811
DOI:	10.1093/bioinformatics/btr381