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Removing noise from pyrosequenced amplicons
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Quince, Christopher, Lanzen, Anders, Davenport, Russell J. and Turnbaugh, Peter J. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, Volume 12 (Number 1). Article number 38. doi:10.1186/1471-2105-12-38 ISSN 1471-2105.
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Official URL: http://dx.doi.org/10.1186/1471-2105-12-38
Abstract
Background
In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs) present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms.
| Item Type: | Journal Article | ||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QP Physiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Genomics , Nucleotide sequence, DNA -- Computer programs, Gene mapping | ||||||||
| Journal or Publication Title: | BMC Bioinformatics | ||||||||
| Publisher: | BioMed Central Ltd. | ||||||||
| ISSN: | 1471-2105 | ||||||||
| Official Date: | 28 February 2011 | ||||||||
| Dates: |
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| Volume: | Volume 12 | ||||||||
| Number: | Number 1 | ||||||||
| Article Number: | Article number 38 | ||||||||
| DOI: | 10.1186/1471-2105-12-38 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Date of first compliant deposit: | 28 December 2015 | ||||||||
| Date of first compliant Open Access: | 28 December 2015 | ||||||||
| Funder: | Engineering and Physical Sciences Research Council (EPSRC), National Institutes of Health (U.S.) (NIH) | ||||||||
| Grant number: | EP/H003851/1(EPSRC), P50GM068763 (NIH) | ||||||||
| Adapted As: |
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