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© 2012 Keegan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, et al. (2012) A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE. PLoS Comput Biol 8(6): e1002541. doi:10.1371/journal.pcbi.1002541

Abstract

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as "noise" or "error") within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms.

Details

Title
A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE
Author
Keegan, Kevin P; Trimble, William L; Wilkening, Jared; Wilke, Andreas; Harrison, Travis; Meyer, Folker
Pages
e1002541
Section
Research Article
Publication year
2012
Publication date
Jun 2012
Publisher
Public Library of Science
ISSN
1553734X
e-ISSN
15537358
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1313185991
Copyright
© 2012 Keegan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, et al. (2012) A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE. PLoS Comput Biol 8(6): e1002541. doi:10.1371/journal.pcbi.1002541