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1. novoalab/SeqTagger novoalab/SeqTagger Public

   Super-fast and accurate demultiplexing of direct RNA-seq runs (Pryszcz*, Diensthuber*, et al., Genome Res 2025)

   Jupyter Notebook 20 2

2. novoalab/modPhred novoalab/modPhred Public

   modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

   Python 16 1

3. novoalab/nanoRMS novoalab/nanoRMS Public

   Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* et al., Nature Biotech 2021)

   Jupyter Notebook 25 11

4. Gabaldonlab/redundans Gabaldonlab/redundans Public

   Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

   C++ 188 23