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Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats

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Bioinformatics Research and Applications (ISBRA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9683))

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Abstract

Advances in the DNA sequencing technology over the past decades have increased the volume of raw sequenced genomic data available for further assembly and analysis. While there exist many software tools for assembly of sequenced genomic material, they often experience difficulties with reconstructing complete chromosomes. Major obstacles include uneven read coverage and long similar subsequences (repeats) in genomes. Assemblers therefore often are able to reliably reconstruct only long subsequences, called scaffolds.

We present a method for simultaneous co-assembly of all fragmented genomes (represented as collections of scaffolds rather than chromosomes) in a given set of annotated genomes. The method is based on the analysis of gene orders and relies on the evolutionary model, which includes genome rearrangements as well as gene insertions and deletions. It can also utilize information about genomic repeats and the phylogenetic tree of the given genomes, further improving their assembly quality.

The work is supported by the National Science Foundation under Grant No. IIS-1462107.

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Notes

  1. 1.

    Since each singleton multicolor mc (i.e., \(|mc|=1\)) is T-consistent, our new method involves independent assembly of single genomes as a particular case.

  2. 2.

    The value of \(\varDelta =1\) corresponds to a typical fusion. We consider potential assembly only if it could achieve a better gain in the evolutionary score than a fusion.

  3. 3.

    Genome Fc is omitted to simulate the case when no closely related reference genome is available.

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Author information

Authors and Affiliations

  1. The George Washington University, Washington, DC, USA

    Sergey Aganezov & Max A. Alekseyev

  2. ITMO University, St. Petersburg, Russia

    Sergey Aganezov

Authors
  1. Sergey Aganezov
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  2. Max A. Alekseyev
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Corresponding author

Correspondence to Max A. Alekseyev .

Editor information

Editors and Affiliations

  1. Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA

    Anu Bourgeois

  2. Centre for Disease Control & Prevention, Atlanta, Georgia, USA

    Pavel Skums

  3. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Xiang Wan

  4. Georgia State University, Atlanta, Georgia, USA

    Alex Zelikovsky

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© 2016 Springer International Publishing Switzerland

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Aganezov, S., Alekseyev, M.A. (2016). Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_20

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_20

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38781-9

  • Online ISBN: 978-3-319-38782-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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