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International Conference on Research in Computational Molecular Biology

RECOMB 2015: Research in Computational Molecular Biology pp 222–223Cite as

ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9029))

Abstract

Next-generation sequencing (NGS) is a powerful technology as it can produce millions of short read pairs covering whole genome; however, a complete genome assembly remains challenging. Usually, assembled genome pieces (i.e., contigs) are merged into chains (i.e., scaffolds) using read pairs mapped to pairs of contigs. A recent comprehensive evaluation of available software shows that the scaffolding problem is still open [1]. In this paper we present a novel scaffolding tool ScaffMatch based on the maximum weight matching of pairs of reverse complement strands representing contigs and further filling the scaffold with skipped short contigs.

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References

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Author information

Authors and Affiliations

  1. Georgia State University, Atlanta, GA, 30303, USA

    Igor Mandric & Alex Zelikovsky

Authors
  1. Igor Mandric
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  2. Alex Zelikovsky
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Corresponding author

Correspondence to Igor Mandric .

Editor information

Editors and Affiliations

  1. National Center of Biotechnology Information, Bethesda, Maryland, USA

    Teresa M. Przytycka

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© 2015 Springer International Publishing Switzerland

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Mandric, I., Zelikovsky, A. (2015). ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. In: Przytycka, T. (eds) Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science(), vol 9029. Springer, Cham. https://doi.org/10.1007/978-3-319-16706-0_22

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  • DOI: https://doi.org/10.1007/978-3-319-16706-0_22

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-16705-3

  • Online ISBN: 978-3-319-16706-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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