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Detection of Highly Variable Genome Fragments in Unmapped Reads of Escherichia coli Genomes

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Bioinformatics and Biomedical Engineering (IWBBIO 2020)

Abstract

Whole-genome sequencing becomes a powerful tool in the study of closely related bacterial population as a single nucleotides changes can be detected. However, the postprocessing of obtained data still remains problematic. Reference-based assembly of genomes only allows identification of shared parts of genomes. Here, we show a pipeline for de novo assembly of unmapped reads and locating variable regions in it. Identified regions can be used as new markers for bacterial genotyping.

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Acknowledgments

This work was supported by grant project of the Czech Science Foundation [GACR 17-01821S].

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Correspondence to Marketa Nykrynova .

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Nykrynova, M., Barton, V., Bezdicek, M., Lengerova, M., Skutkova, H. (2020). Detection of Highly Variable Genome Fragments in Unmapped Reads of Escherichia coli Genomes. In: Rojas, I., Valenzuela, O., Rojas, F., Herrera, L., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2020. Lecture Notes in Computer Science(), vol 12108. Springer, Cham. https://doi.org/10.1007/978-3-030-45385-5_51

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  • DOI: https://doi.org/10.1007/978-3-030-45385-5_51

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  • Online ISBN: 978-3-030-45385-5

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