TL;DR

Signal-to-sequence alignments like Remora, but faster and more accessible. Download fishnet, extract the binary and run the align command:

./fishnet align --help

For further processing, run the reformat command:

./fishnet reformat --help

Documentation

Detailed documentation is provided here.

Repository structure

The code-base is split into different libraries:

• fishnet: Contains the entry point to the command line interface
• alignment: Contains the signal-to-sequence alignment logic
• reformat: Contains the reformatting logic
• pod5_reader_api: Contains the logic for accessing pod5 data
• helper: Contains helper scripts used in the alignment and reformat libraries

Beyond the code the repo contains example data to test fishnet, and detailled documentation of all libraries.

TODOs

• Output optimization: At the moment, the single writer thread seems to be a bottleneck. It might help to have each worker thread write to separate tempfiles and then merge these into one at the end.
• Look into the differences between varying refinement iterations to determine the best default value

License

This project is licensed under the GPL3.0 License. See the LICENSE file for details.

Citation

Fishnet is currently under review in Genome Biology:

DOI: https://doi.org/10.21203/rs.3.rs-8345719/v1

If you use Fishnet in your work, we would be really happy if you cite us:

Vincent Dietrich, Lioba Lehmann, Stefan Pastore et al. Fishnet simplifies and accelerates signal-to-sequence alignment in Nanopore sequencing, 16 January 2026, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-8345719/v1]