Raw nanopore squiggle alignment for bacterial typing distinction enhancement

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F21%3APU142168" target="_blank" >RIV/00216305:26220/21:PU142168 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1109/BIBM52615.2021.9669632" target="_blank" >http://dx.doi.org/10.1109/BIBM52615.2021.9669632</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/BIBM52615.2021.9669632" target="_blank" >10.1109/BIBM52615.2021.9669632</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Raw nanopore squiggle alignment for bacterial typing distinction enhancement

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Raw nanopore squiggle alignment for bacterial typing distinction enhancement

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

30502 - Other medical science

Projekt

<a href="/cs/project/EF19_073%2F0016948" target="_blank" >EF19_073/0016948: Kvalitní interní granty VUT</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2021

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

ISBN

978-1-6654-0126-5

ISSN

—

e-ISSN

—

Počet stran výsledku

6

Strana od-do

1969-1974

Název nakladatele

Neuveden

Místo vydání

neuveden

Místo konání akce

Houston, Texas

Datum konání akce

9. 12. 2021

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

—