Novoa Lab

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1. nanoRMS 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

2. EpiNano EpiNano Public

   Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

   Python 118 35

3. Nano3P_Seq Nano3P_Seq Public

   Nanopore 3' end-capture sequencing (Begik et al., Nat Methods 2022)

   Python 15 3

4. m6ABasecaller m6ABasecaller Public

   An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

   Jupyter Notebook 18 2

5. Nano-tRNAseq Nano-tRNAseq Public

   Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)

   Python 17 5

6. SeqTagger SeqTagger Public

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

   Jupyter Notebook 20 2