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BUSCO: Assessing Genome Assembly and Annotation Completeness

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Gene Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1962))

Abstract

Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.

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Acknowledgments

We would like to thank all members of the Zdobnov group, in particular Felipe Simão and Christopher Rands for their useful comments. This work was partly supported by the Swiss Institute of Bioinformatics SER funding and the Swiss National Science Foundation funding 31003A_166483 to E.Z.

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Authors and Affiliations

  1. Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland

    Mathieu Seppey, Mosè Manni & Evgeny M. Zdobnov

Authors
  1. Mathieu Seppey
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  2. Mosè Manni
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  3. Evgeny M. Zdobnov
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Corresponding author

Correspondence to Evgeny M. Zdobnov .

Editor information

Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany

    Martin Kollmar

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Seppey, M., Manni, M., Zdobnov, E.M. (2019). BUSCO: Assessing Genome Assembly and Annotation Completeness. In: Kollmar, M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9173-0_14

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  • DOI: https://doi.org/10.1007/978-1-4939-9173-0_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9172-3

  • Online ISBN: 978-1-4939-9173-0

  • eBook Packages: Springer Protocols

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