Fishnet simplifies and accelerates signal-to-sequence alignment in Nanopore sequencing

Nanopore sequencing preserves native DNA and RNA modifications and encodes them directly in electrical signal, but extracting this information requires accurate signal-to-sequence alignment. Existing tools perform this reliably yet often demand metadata handling or format conversion. We present Fishnet, a lightweight and fast aligner that reimplements the Remora alignment algorithm while removing surrounding overhead. Fishnet produces near-identical alignments more than thirty times faster and provides a simple command-line interface for alignment and downstream formatting. Benchmarks demonstrate high concordance between alignment tools and Fishnet’s mostly superior speed. Analyses of synthetic RNA constructs prove its practical utility for streamlined studies of modified nucleotides.