Assembly of long error-prone reads using de Bruijn graphs
The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph appr...
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| Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 113; no. 52; pp. E8396 - E8405 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
National Academy of Sciences
27.12.2016
|
| Series | PNAS Plus |
| Subjects | |
| Online Access | Get full text |
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| Abstract | The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions. |
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| AbstractList | The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions. When the long reads generated using single-molecule se-quencing (SMS) technology were made available, most researchers were skeptical about the ability of existing algorithms to generate high-quality assemblies from long error-prone reads. Nevertheless, recent algorithmic breakthroughs resulted in many successful SMS sequencing projects. However, as the recent assemblies of important plant pathogens illustrate, the problem of assembling long error-prone reads is far from being resolved even in the case of relatively short bacterial genomes. We propose an algorithmic approach for assembling long error-prone reads and describe the ABruijn assembler, which results in accurate genome reconstructions. The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions. The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions. |
| Author | Lin, Yu Pevzner, Pavel A. Kolmogorov, Mikhail Shen, Max W. Chaisson, Mark Yuan, Jeffrey |
| Author_xml | – sequence: 1 givenname: Yu surname: Lin fullname: Lin, Yu organization: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092 – sequence: 2 givenname: Jeffrey surname: Yuan fullname: Yuan, Jeffrey organization: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092 – sequence: 3 givenname: Mikhail surname: Kolmogorov fullname: Kolmogorov, Mikhail organization: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092 – sequence: 4 givenname: Max W. surname: Shen fullname: Shen, Max W. organization: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092 – sequence: 5 givenname: Mark surname: Chaisson fullname: Chaisson, Mark organization: Department of Genome Sciences, University of Washington, Seattle, WA 98105 – sequence: 6 givenname: Pavel A. surname: Pevzner fullname: Pevzner, Pavel A. organization: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092 |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27956617$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | Volumes 1–89 and 106–113, copyright as a collective work only; author(s) retains copyright to individual articles Copyright National Academy of Sciences Dec 27, 2016 |
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| Title | Assembly of long error-prone reads using de Bruijn graphs |
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