MANASIG: Python Package to MAnipulateNAnopore SIGnals from sequencing files

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F21%3APU142140" target="_blank" >RIV/00216305:26220/21:PU142140 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1109/BIBM52615.2021.9669821" target="_blank" >http://dx.doi.org/10.1109/BIBM52615.2021.9669821</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/BIBM52615.2021.9669821" target="_blank" >10.1109/BIBM52615.2021.9669821</a>

Jazyk výsledku

angličtina

Název v původním jazyce

MANASIG: Python Package to MAnipulateNAnopore SIGnals from sequencing files

Popis výsledku v původním jazyce

Sequencing technology allows us to study the structure and function of several genomic processes. Recently, nanopore sequencing technology has become widely used. It allows us to study a single molecule's structure and provide reads several times longer than previously used second sequencer generation methods. However, the error rate is still higher, which limits further analysis. The main source of errors is in the base-calling process. Nanopore sequencers produce a digital signal based on the electric potential's alternations on the pore. The signal then needs to be translated to the sequence of characters representing the nucleotides. The Base-calling process is still improving, but there is a potential to bypass it and process the raw signal data as the carrier of the sequenced molecule information. Thus we present a Python package designed to manipulate, extract and process nanopore sequencing files and provide a helpful tool to analyze squiggles. It provides a single API to access the reads attributes allowing extraction and signal visualization. The package can work with base-called data and provide a known BLAST search process to select specific regions of interest. The package is available at: https://github.com/VojtechBarton/manasig

Název v anglickém jazyce

MANASIG: Python Package to MAnipulateNAnopore SIGnals from sequencing files

Popis výsledku anglicky

Sequencing technology allows us to study the structure and function of several genomic processes. Recently, nanopore sequencing technology has become widely used. It allows us to study a single molecule's structure and provide reads several times longer than previously used second sequencer generation methods. However, the error rate is still higher, which limits further analysis. The main source of errors is in the base-calling process. Nanopore sequencers produce a digital signal based on the electric potential's alternations on the pore. The signal then needs to be translated to the sequence of characters representing the nucleotides. The Base-calling process is still improving, but there is a potential to bypass it and process the raw signal data as the carrier of the sequenced molecule information. Thus we present a Python package designed to manipulate, extract and process nanopore sequencing files and provide a helpful tool to analyze squiggles. It provides a single API to access the reads attributes allowing extraction and signal visualization. The package can work with base-called data and provide a known BLAST search process to select specific regions of interest. The package is available at: https://github.com/VojtechBarton/manasig

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

7

Strana od-do

1941-1947

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

—