Publication detail

Raw nanopore squiggle alignment for bacterial typing distinction enhancement

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

Original Title

Raw nanopore squiggle alignment for bacterial typing distinction enhancement

Type

conference paper

Language

English

Original Abstract

Nanopore sequencing is coming to the fore as it can produce long reads. However, the error rate is still high, which limits the use of this platform. The main source of error is basecalling, where raw current signals are converted to nucleotide sequences. If analysis of the raw signals were done, the error rate could be significantly lower. Here we show the use of dynamic time warping for raw squiggle analysis. The squiggles passing through the pore have different speeds; thus, the signal lengths are also different. If we align the signals using dynamic time warping, the squiggles themselves can be analyzed, and the basecalling process can be omitted. The advantage of squiggle analysis is that the nanopore signals can have even higher variability than the nucleotide sequences as they can be chemically or epigenetically modified. Thus, distinguishing bacterial strains that differ in only a few nucleotides in the whole genome will be possible.

Keywords

nanopore sequencing; squiggles; dynamic time warping; bacterial typing

Authors

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

Released

9. 12. 2021

ISBN

978-1-6654-0126-5

Book

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Pages from

1969

Pages to

1974

Pages count

6

BibTex

@inproceedings{BUT173238,
  author="Markéta {Jakubíčková} and Vojtěch {Bartoň} and Martin {Vítek} and Matěj {Bezdíček} and Martina {Lengerová} and Helena {Vítková}",
  title="Raw nanopore squiggle alignment for bacterial typing distinction enhancement",
  booktitle="2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)",
  year="2021",
  pages="1969--1974",
  doi="10.1109/BIBM52615.2021.9669632",
  isbn="978-1-6654-0126-5"
}