NANOBLAST: Python Tool for Raw Nanopore Signal Processing
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Date
2024
Authors
Suriak, Martin
Nykrýnová, Markéta
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Mark
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Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií
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.
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Proceedings I of the 30st Conference STUDENT EEICT 2024: General papers. s. 24-27. ISBN 978-80-214-6231-1
https://www.eeict.cz/eeict_download/archiv/sborniky/EEICT_2024_sbornik_1.pdf
https://www.eeict.cz/eeict_download/archiv/sborniky/EEICT_2024_sbornik_1.pdf
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Peer-reviewed
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en
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© Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií