UCHIME improves sensitivity and speed of chimera detection

Robert C. Edgar, Brian J. Haas, Jose C. Clemente, Christopher Quince, Rob Knight

Research output: Contribution to journalArticlepeer-review

9668 Citations (SciVal)

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.

Original languageEnglish
Pages (from-to)2194-2200
Number of pages7
JournalBioinformatics
Volume27
Issue number16
DOIs
Publication statusPublished - Aug 2011

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