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International Workshop on Frontiers in Algorithmics

FAW 2015: Frontiers in Algorithmics pp 150–161Cite as

On the Sound Covering Cycle Problem in Paired de Bruijn Graphs

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9130))

Abstract

Paired de Bruijn graphs are a variant of classic de Bruijn graphs used in genome assembly. In these graphs, each vertex \(v\) is associated with two labels \(\mathcal{L}(v)\) and \(\mathcal{R}(v)\). We study the NP-hard Sound Covering Cycle problem which has as input a paired de Bruijn graph \(G\) and two integers \(d\) and \(\ell \), and the task is to find a length-\(\ell \) cycle \(C\) containing all arcs of \(G\) such that for every vertex \(v\) in \(C\) and the vertex \(u\) which occurs exactly \(d\) positions after \(v\) in \(C\), we have \(\mathcal{R}(v)=\mathcal{L}(u)\). We present the first exact algorithms for this problem and several variants.

C. Komusiewicz – Partially supported by the DAAD Procope program (project 55934856).

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References

  1. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., et al.: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477 (2012)

    Article  MathSciNet  Google Scholar 

  2. Böcker, S., Lipták, Z.: A fast and simple algorithm for the money changing problem. Algorithmica 48(4), 413–432 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  3. Earl, D., Bradnam, K., John, J.S., Darling, A., Lin, D., Fass, J., Yu, H.O.K., Buffalo, V., Zerbino, D.R., Diekhans, M., et al.: Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21(12), 2224–2241 (2011)

    Article  Google Scholar 

  4. Edmonds, J., Johnson, E.L.: Matching, Euler tours and the Chinese postman. Math. Program. 5(1), 88–124 (1973)

    Article  MATH  MathSciNet  Google Scholar 

  5. Haiminen, N., Kuhn, D.N., Parida, L., Rigoutsos, I.: Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS One 6(9), e24182 (2011)

    Article  Google Scholar 

  6. Idury, R.M., Waterman, M.S.: A new algorithm for DNA sequence assembly. J. Comput. Biol. 2(2), 291–306 (1995)

    Article  Google Scholar 

  7. Kapun, E., Tsarev, F.: On NP-hardness of the paired de Bruijn sound cycle problem. In: Darling, A., Stoye, J. (eds.) WABI 2013. LNCS, vol. 8126, pp. 59–69. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  8. Medvedev, P., Pham, S., Chaisson, M., Tesler, G., Pevzner, P.: Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J. Comput. Biol. 18(11), 1625–1634 (2011)

    Article  MathSciNet  Google Scholar 

  9. Pevzner, P.A., Tang, H., Waterman, M.S.: An Eulerian path approach to DNA fragment assembly. Proc. Nat. Acad. Sci. 98(17), 9748–9753 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  10. Prjibelski, A.D., Vasilinetc, I., Bankevich, A., Gurevich, A., Krivosheeva, T., Nurk, S., Pham, S., Korobeynikov, A., Lapidus, A., Pevzner, P.A.: ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics 30(12), i293–i301 (2014)

    Article  Google Scholar 

  11. Salzberg, S.L., Phillippy, A.M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T.J., Schatz, M.C., Delcher, A.L., Roberts, M., et al.: GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22(3), 557–567 (2012)

    Article  Google Scholar 

  12. Vyahhi, N., Pyshkin, A., Pham, S., Pevzner, P.A.: From de Bruijn graphs to rectangle graphs for genome assembly. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 249–261. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  13. Zhang, W., Chen, J., Yang, Y., Tang, Y., Shang, J., Shen, B.: A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One 6(3), e17915 (2011)

    Article  Google Scholar 

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Authors and Affiliations

  1. Institut für Softwaretechnik und Theoretische Informatik, TU Berlin, Berlin, Germany

    Christian Komusiewicz

  2. LINA - UMR CNRS 6241, Université de Nantes, Saint-Nazaire, France

    Andreea Radulescu

Authors
  1. Christian Komusiewicz
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  2. Andreea Radulescu
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Correspondence to Christian Komusiewicz .

Editor information

Editors and Affiliations

  1. Central South University, Changsha, China

    Jianxin Wang

  2. Courant Institute, New York University, New York, New York, USA

    Chee Yap

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© 2015 Springer International Publishing Switzerland

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Komusiewicz, C., Radulescu, A. (2015). On the Sound Covering Cycle Problem in Paired de Bruijn Graphs. In: Wang, J., Yap, C. (eds) Frontiers in Algorithmics. FAW 2015. Lecture Notes in Computer Science(), vol 9130. Springer, Cham. https://doi.org/10.1007/978-3-319-19647-3_14

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  • DOI: https://doi.org/10.1007/978-3-319-19647-3_14

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19646-6

  • Online ISBN: 978-3-319-19647-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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