NANOSLAST: Nanopore Signal Local Alignment and Segmentation Tool

NANOSLAST: Nanopore Signal Local Alignment and Segmentation Tool

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Nanopore sequencing provided by Oxford Nanopore Technologies enables real-time analysis of native DNA or RNA molecules based on measured electrical signals called squiggles. While basecalling algorithms translate squiggles into nucleotide sequences, much of the raw signal information remains unexplored. Although several tools exist for inspecting the squiggles and offer simple signal visualization, they do not provide integrated workflows that allow users to search for specific nucleotide sequences and directly extract or visualize the corresponding raw signal segments. To address this gap, we developed NANOSLAST – a Nanopore Signal Local Alignment and Search Tool. This Python-based tool links local sequence similarity searches (via BLAST) to raw nanopore signals using basecalled SAM files and signal data from FAST5 or POD5 formats. The tool can be used to extract signals corresponding to specific motifs or functional elements, compare raw signal characteristics between different flowcells or sequencers or extract signal– sequence pairs suitable for training machine learning models focused on basecalling, methylation detection or other purposes.

Nanopore sequencing provided by Oxford Nanopore Technologies enables real-time analysis of native DNA or RNA molecules based on measured electrical signals called squiggles. While basecalling algorithms translate squiggles into nucleotide sequences, much of the raw signal information remains unexplored. Although several tools exist for inspecting the squiggles and offer simple signal visualization, they do not provide integrated workflows that allow users to search for specific nucleotide sequences and directly extract or visualize the corresponding raw signal segments. To address this gap, we developed NANOSLAST – a Nanopore Signal Local Alignment and Search Tool. This Python-based tool links local sequence similarity searches (via BLAST) to raw nanopore signals using basecalled SAM files and signal data from FAST5 or POD5 formats. The tool can be used to extract signals corresponding to specific motifs or functional elements, compare raw signal characteristics between different flowcells or sequencers or extract signal– sequence pairs suitable for training machine learning models focused on basecalling, methylation detection or other purposes.

nanopore sequencing; squiggle; signal processing; BLAST; pod5; fast5

nanopore sequencing; squiggle; signal processing; BLAST; pod5; fast5

JAKUBÍČKOVÁ, M.; ZBUDILOVÁ, M.; SURIAK, M.; VÍTKOVÁ, H.

17.08.2025

Avestia Publishing

978-1-990800-61-0

Proceedings of the World Congress on Electrical Engineering and Computer Systems and Science

4

https://international-aset.net/avestia.com/EECSS2025_Proceedings/files/paper/ICBES/ICBES_151.pdf