Name
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. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/bioinformatics/btr381 | Bioinformatics |
Field | DocType | Volume |
mothur,UniFrac,Polymerase chain reaction,Biology,16S ribosomal RNA,Chimera (genetics),DNA sequencing,Bioinformatics,Tenericutes,Internal transcribed spacer | Journal | 27 |
Issue | ISSN | Citations |
16 | 1367-4803 | 44 |
PageRank | References | Authors |
3.02 | 6 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Robert C. Edgar | 1 | 611 | 53.19 |
| Brian J. Haas | 2 | 92 | 6.75 |
| Jose C. Clemente | 3 | 44 | 3.02 |
| Christopher Quince | 4 | 126 | 9.15 |
| Rob Knight | 5 | 366 | 26.19 |