A. A. Sergushichev, A. V. Alexandrov, S. V. Kazakov, F. N. Tsarev, A. A. Shalyto, “Combining de Bruijn graphs, overlap graphs and microassembly for <i>de novo</i> genome assembly”, Izv. Saratov Univ. Math. Mech. Inform., 2013, Volume 13, Issue 2(2),Pages <nobr>51

This article is cited in 4 papers

Computer science

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

A. A. Sergushichev^a, A. V. Alexandrov^a, S. V. Kazakov^a, F. N. Tsarev^b, A. A. Shalyto^c

^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

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.

UDC: 004.021

DOI: 10.18500/1816-9791-2013-13-2-2-51-57