Publication detail

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

NYKRÝNOVÁ, M. BARTOŇ, V. BEZDÍČEK, M. LENGEROVÁ, M. ŠKUTKOVÁ, H.

Original Title

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

English Title

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

Type

conference paper

Language

en

Original 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.

English 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.

Keywords

genome assembly; unmapped reads; genotyping

Released

06.05.2020

ISBN

978-3-030-45384-8

Book

Bioinformatics and Biomedical Engineering

Pages from

569

Pages to

578

Pages count

10

BibTex


@inproceedings{BUT163867,
  author="Markéta {Nykrýnová} and Vojtěch {Bartoň} and Matěj {Bezdíček} and Martina {Lengerová} and Helena {Škutková}",
  title="Detection of Highly Variable Genome Fragments in Unmapped Reads of Escherichia coli Genomes",
  annote="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.",
  booktitle="Bioinformatics and Biomedical Engineering",
  chapter="163867",
  doi="10.1007/978-3-030-45385-5_51",
  howpublished="print",
  year="2020",
  month="may",
  pages="569--578",
  type="conference paper"
}