NANOBLAST: Python Tool for Raw Nanopore Signal Processing

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.