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2020 | OriginalPaper | Chapter

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

Authors : Marketa Nykrynova, Vojtech Barton, Matej Bezdicek, Martina Lengerova, Helena Skutkova

Published in: Bioinformatics and Biomedical Engineering

Publisher: Springer International Publishing

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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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Title: Detection of Highly Variable Genome Fragments in Unmapped Reads of Escherichia coli Genomes
Authors: Marketa Nykrynova
Vojtech Barton
Matej Bezdicek
Martina Lengerova
Helena Skutkova
Publisher: Springer International Publishing
Book: Bioinformatics and Biomedical Engineering
Print ISBN: 978-3-030-45384-8

Electronic ISBN: 978-3-030-45385-5

Copyright Year: 2020
DOI: https://doi.org/10.1007/978-3-030-45385-5_51

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