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Getting started

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Fishnet performs signal-to-sequence alignment (resquiggling) fast and accessibly. It uses the alignment algorithm from ONT's Remora.

Installation

See Installation for all details.

Alignment

fishnet align \
  --bam <basecalls.bam> \
  --pod5 <raw-signal.pod5> \
  --out <output-file>

See Align for an overview.

Reformatting

fishnet reformat \
  --alignment <alignments.parquet> \
  --pod5 <raw-signal.pod5> \
  --motifs <motif> \
  --out <output-file>

See Reformat for an overview.

POD5 Reader API

See Pod5 Reader API for an overview.

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]