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Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT)

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Research in Computational Molecular Biology (RECOMB 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13278))

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Abstract

Recent assemblies by the T2T and VGP consortia have achieved significant accuracy but required a tremendous amount of effort and resources.

A full version of this paper is available as a preprint https://doi.org/10.1101/2022.01.20.477068.

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References

  1. Tomescu, A.I., Medvedev, P.: Safe and complete contig assembly via omnitigs. In: Singh, M. (ed.) RECOMB 2016. LNCS, vol. 9649, pp. 152–163. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-31957-5_11

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  2. Cairo, M., Khan, S., Rizzi, R., Schmidt, S., Tomescu, A.I., Zirondelli, E.C.: The hydrostructure: a Universal Framework for Safe and Complete Algorithms for Genome Assembly, arXiv preprint arXiv:2011.12635 (2020)

  3. Rahman, A., Medvedev, P.: Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful, bioRxiv (2022)

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Penn State, University Park, USA

    Amatur Rahman & Paul Medvedev

  2. Department of Biochemistry and Molecular Biology, Penn State, University Park, USA

    Paul Medvedev

  3. Center for Computational Biology and Bioinformatics, Penn State, University Park, USA

    Paul Medvedev

Authors
  1. Amatur Rahman
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  2. Paul Medvedev
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Corresponding authors

Correspondence to Amatur Rahman or Paul Medvedev .

Editor information

Editors and Affiliations

  1. Columbia University, New York, NY, USA

    Itsik Pe'er

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© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

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Rahman, A., Medvedev, P. (2022). Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). In: Pe'er, I. (eds) Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science(), vol 13278. Springer, Cham. https://doi.org/10.1007/978-3-031-04749-7_35

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  • DOI: https://doi.org/10.1007/978-3-031-04749-7_35

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-04748-0

  • Online ISBN: 978-3-031-04749-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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