UCHIME improves sensitivity and speed of chimera detection

Bioinformatics - Tập 27 Số 16 - Trang 2194-2200 - 2011
Robert C. Edgar1, Brian J. Haas1, José C. Clemente1, Christopher Quince1, Rob Knight1
11 Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK

Tóm tắt

Abstract 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:  [email protected] Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information:  Supplementary data are available at Bioinformatics online.

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Bioinformatics

Tập 27 Số 16

2194-2200

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