Publication detail

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

SURIAK, M. NYKRÝNOVÁ, M.

Original Title

NANOBLAST: Python Tool for Raw Nanopore Signal Processing

Type

article in a collection out of WoS and Scopus

Language

English

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.

Keywords

squiggle; sequencing; signal processing

Authors

SURIAK, M.; NYKRÝNOVÁ, M.

Released

23. 4. 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"
}