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Izvestiya of Saratov University. Mathematics. Mechanics. Informatics, 2013, Volume 13, Issue 2(2), Pages 51–57
DOI: https://doi.org/10.18500/1816-9791-2013-13-2-2-51-57 (Mi isu413) 		 
This article is cited in 4 scientific papers (total in 4 papers)

Computer science

Combining de Bruijn graphs, overlap graphs and microassembly for de novo genome assembly

A. A. Sergushicheva, A. V. Alexandrova, S. V. Kazakova, F. N. Tsarevb, A. A. Shalytoc

a Saint-Petersburg National Research University of Information Technologies, Mechanics and Optics, Russia, 197101, St. Petersburg, Kronverkskiy pr., 49
b Saint-Petersburg National Research University of Information Technologies, Mechanics and Optics, Russia, 197101, St. Petersburg, Kronverkskiy pr., 49
c Saint-Petersburg National Research University of Information Technologies, Mechanics and Optics, Russia, 197101, St. Petersburg, Kronverkskiy pr., 49
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DOI: https://doi.org/10.18500/1816-9791-2013-13-2-2-51-57
Abstract: In this paper we present a method for de novo genome assembly that splits the process into three stages: quasicontig assembly; contig assembly from quasicontigs; contig postprocessing with microassembly. The first stage uses de Bruijn graph, the second one uses overlap graph. We have carried out experiments of assembling the E. Coli genome (size $\approx4.5$ Mbp) and Maylandia zebra genome (size $\approx1$ Gbp). Advantage of proposed method is a low memory consumption.
Key words: genome assembly, contigs, de Bruijn graph, overlap graph, microassembly.
Bibliographic databases:
Document Type: Article
UDC: 004.021
Language: Russian
Citation: A. A. Sergushichev, A. V. Alexandrov, S. V. Kazakov, F. N. Tsarev, A. A. Shalyto, “Combining de Bruijn graphs, overlap graphs and microassembly for de novo genome assembly”, Izv. Saratov Univ. Math. Mech. Inform., 13:2(2) (2013), 51–57
Citation in format AMSBIB
\Bibitem{SerAleKaz13}
\by A.~A.~Sergushichev, A.~V.~Alexandrov, S.~V.~Kazakov, F.~N.~Tsarev, A.~A.~Shalyto
\paper Combining de Bruijn graphs, overlap graphs and microassembly for \textit{de novo} genome assembly
\jour Izv. Saratov Univ. Math. Mech. Inform.
\yr 2013
\vol 13
\issue 2(2)
\pages 51--57
\mathnet{http://mi.mathnet.ru/isu413}
\crossref{https://doi.org/10.18500/1816-9791-2013-13-2-2-51-57}
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  • https://www.mathnet.ru/eng/isu/v13/i4/p51
    • This publication is cited in the following 4 articles:
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
    		Известия Саратовского университета. Новая серия. Серия Математика. Механика. Информатика
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    Full-text PDF :127
    References:51
     
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