Detail publikačního výsledku

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

SURIAK, M.; NYKRÝNOVÁ, M.

Originální název

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

Anglický název

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

Druh

Stať ve sborníku mimo WoS a Scopus

Originální abstrakt

Oxford Nanopore Technologies’ sequencers enable direct real-time DNA/RNA sequencing. While numerous tools aid in analyzing the nanopore output data, offering functions such as visualizing raw signals with highlighted nucleotide positions, none provide a complete solution for exporting analyzed data into a clear, comprehensive file. In response, a Python tool has been developed to streamline various tasks. This includes searching for specific nucleotide sequences using BLAST, plotting raw signals with detected nucleotide bases, and generating a comprehensive file containing all essential information. The tool integrates components for handling raw nanopore data, extracting crucial information from the basecalling process using SAM file handlers, and utilizing a BLAST search engine. Employing a comprehensive algorithm, it can handle both the old FAST5 and the novel POD5 formats, enabling the identification of any nucleotide sequence and its corresponding signal.

Anglický abstrakt

Oxford Nanopore Technologies’ sequencers enable direct real-time DNA/RNA sequencing. While numerous tools aid in analyzing the nanopore output data, offering functions such as visualizing raw signals with highlighted nucleotide positions, none provide a complete solution for exporting analyzed data into a clear, comprehensive file. In response, a Python tool has been developed to streamline various tasks. This includes searching for specific nucleotide sequences using BLAST, plotting raw signals with detected nucleotide bases, and generating a comprehensive file containing all essential information. The tool integrates components for handling raw nanopore data, extracting crucial information from the basecalling process using SAM file handlers, and utilizing a BLAST search engine. Employing a comprehensive algorithm, it can handle both the old FAST5 and the novel POD5 formats, enabling the identification of any nucleotide sequence and its corresponding signal.

Klíčová slova

squiggle; sequencing; signal processing

Klíčová slova v angličtině

squiggle; sequencing; signal processing

Autoři

SURIAK, M.; NYKRÝNOVÁ, M.

Vydáno

23.04.2024

Nakladatel

Brno University of Technology, Faculty of Electrical Engineering and Communication

Místo

Brno, Czech Republic

ISBN

978-80-214-6231-1

Kniha

Proceedings I of the 30th Conference STUDENT EEICT 2024

Edice

1

Strany od

24

Strany do

27

Strany počet

4

URL

https://www.eeict.cz/eeict_download/archiv/sborniky/EEICT_2024_sbornik_1.pdf

BibTex

@inproceedings{BUT188940,
  author="Martin {Suriak} and Markéta {Jakubíčková}",
  title="NANOBLAST: Python Tool for Raw Nanopore Signal Processing",
  booktitle="Proceedings I of the 30th Conference STUDENT EEICT 2024",
  year="2024",
  series="1",
  pages="24--27",
  publisher="Brno University of Technology, Faculty of Electrical Engineering and Communication",
  address="Brno, Czech Republic",
  isbn="978-80-214-6231-1",
  url="https://www.eeict.cz/eeict_download/archiv/sborniky/EEICT_2024_sbornik_1.pdf"
}