Publication result detail

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

SURIAK, M.; NYKRÝNOVÁ, M.

Original Title

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

English Title

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

Type

Paper in proceedings outside WoS and Scopus

Original Abstract

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.

English abstract

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.

Keywords

squiggle; sequencing; signal processing

Key words in English

squiggle; sequencing; signal processing

Authors

SURIAK, M.; NYKRÝNOVÁ, M.

Released

23.04.2024

Publisher

Brno University of Technology, Faculty of Electrical Engineering and Communication

Location

Brno, Czech Republic

ISBN

978-80-214-6231-1

Book

Proceedings I of the 30th Conference STUDENT EEICT 2024

Edition

1

Pages from

24

Pages to

27

Pages count

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"
}