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PacBio-Based Protocol for Bacterial Genome Assembly

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2242))

Abstract

Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline based on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six Dickeya solani genomes, while the assembly process was run just on a slightly improved desktop computer.

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Acknowledgments

All sequencing and comparative genomics research tasks were conducted thanks to founding from National Science Centre in Poland via 2014/14/M/NZ8/00501 granted to E.L. A.M.P. is supported from National Science Centre in Poland via 2016/21/N/NZ1/02783.

Author information

Author notes

  1. Sabina Zoledowska

    Present address: Institute of Biotechnology and Molecular Medicine, Gdansk, Poland

Authors and Affiliations

  1. Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, Poland

    Agata Motyka-Pomagruk, Sabina Zoledowska & Ewa Lojkowska

  2. Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland

    Michal Kabza

Authors
  1. Agata Motyka-Pomagruk
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  2. Sabina Zoledowska
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  3. Michal Kabza
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  4. Ewa Lojkowska
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Corresponding author

Correspondence to Ewa Lojkowska .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Alessio Mengoni

  2. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Giovanni Bacci

  3. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Marco Fondi

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Motyka-Pomagruk, A., Zoledowska, S., Kabza, M., Lojkowska, E. (2021). PacBio-Based Protocol for Bacterial Genome Assembly. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1098-5

  • Online ISBN: 978-1-0716-1099-2

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