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 inProceedings of the National Academy of Sciences - PNAS Vol. 113; no. 52; pp. E8396 - E8405
Main Authors Lin, Yu, Yuan, Jeffrey, Kolmogorov, Mikhail, Shen, Max W., Chaisson, Mark, Pevzner, Pavel A.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 27.12.2016
SeriesPNAS Plus
Subjects
Biological Sciences
Computer science
Errors
Genomes
Graph representations
Physical Sciences
PNAS Plus
de Bruijn graph
single-molecule sequencing
genome assembly
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Summary: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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Edited by Michael S. Waterman, University of Southern California, Los Angeles, CA, and approved October 6, 2016 (received for review March 23, 2016)
Author contributions: Y.L., J.Y., M.K., and P.A.P. designed research; Y.L., J.Y., M.K., M.W.S., and P.A.P. performed research; Y.L., M.K., and M.C. analyzed data; and Y.L., M.K., and P.A.P. wrote the paper.
1Y.L., J.Y., and M.K. contributed equally to this work.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1604560113