Format

Send to

Choose Destination
Bioinformatics. 2011 Aug 15;27(16):2194-200. doi: 10.1093/bioinformatics/btr381. Epub 2011 Jun 23.

UCHIME improves sensitivity and speed of chimera detection.

Author information

1
Tiburon, CA, USA. robert@drive5.com

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:

robert@drive5.com

AVAILABILITY:

Source, binaries and data: http://drive5.com/uchime.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21700674
PMCID:
PMC3150044
DOI:
10.1093/bioinformatics/btr381
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center