Raw nanopore squiggle alignment for bacterial typing distinction enhancement

Result code in 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>
Result on the web
<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>

Result language
angličtina
Original language name
Raw nanopore squiggle alignment for bacterial typing distinction enhancement
Original language description
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.
Czech name
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Czech description
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Project
<a href="/en/project/EF19_073%2F0016948" target="_blank" >EF19_073/0016948: Quality internal grants at BUT</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
ISBN
978-1-6654-0126-5
ISSN
—
e-ISSN
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Number of pages
6
Pages from-to
1969-1974
Publisher name
Neuveden
Place of publication
neuveden
Event location
Houston, Texas
Event date
Dec 9, 2021
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
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