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    36 repositories

    • ONT_basecalling_models

      Public
      Benchmarking of ONT basecalling models for RNA modification detection
      R
      •0•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • tRIBO-seq

      Public
      This is a repo for the analysis related to the ribo-embedded manuscript. The idea is to harmonise the analysis and have a more or less ready-to-go repo to accom…
      R
      •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

    • firstseq

      Public
      Analysis repository for FIRST-seq
      R
      •0•0•0•0•Updated Dec 31, 2025Dec 31, 2025

    • m6ABasecaller

      Public
      An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioR…
      nanoporernam6a-rna-modifications
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•18•3•0•Updated Sep 1, 2025Sep 1, 2025

    • SeqTagger

      Public
      Super-fast and accurate demultiplexing of direct RNA-seq runs.
      nanoporesequencingrnadirectdemultiplexing
      Jupyter Notebook
      •
      Other
      •2•18•0•0•Updated Jul 22, 2025Jul 22, 2025

    • EpiNano

      Public
      Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
      nanoporerna-sequencingm6am6a-rna-modificationsdirect-rna
      Python
      •
      GNU General Public License v2.0
      •33•118•6•2•Updated Jul 8, 2025Jul 8, 2025

    • Nano3P_Seq

      Public
      Nanopore 3' end-capture sequencing (Begik et al., bioRxiv 2021)
      Python
      •
      MIT License
      •3•14•1•0•Updated Jul 7, 2025Jul 7, 2025

    • NanoConsensus

      Public
      R
      •
      MIT License
      •1•2•0•0•Updated Feb 12, 2025Feb 12, 2025

    • nanoRMS2

      Public
      nanoRMS2 is a pipeline for detection of DNA/RNA modifications from raw ONT data
      machine-learningnanoporednasemi-supervised-learningrnafeaturesstoichiometryfast5modificationsbasecalling
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Feb 5, 2025Feb 5, 2025

    • RMaP_challenge

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • polyTailor

      Public
      Poly-A tail length estimation from Nano3P-seq libraries
      Jupyter Notebook
      •0•5•1•0•Updated Nov 11, 2024Nov 11, 2024

    • epitranscriptomic_fingerprinting

      Public
      Scripts used Milenkovic et al. "Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures" (Mol Cell 2024)
      R
      •0•0•1•0•Updated Nov 8, 2024Nov 8, 2024

    • Nano-tRNAseq

      Public
      Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)
      Python
      •
      GNU General Public License v3.0
      •5•16•3•0•Updated Sep 19, 2024Sep 19, 2024

    • basecalling_models

      Public
      Benchmarked base calling models for nanopore sequencing providing super high accuracy and improved RNA modification detection
      R
      •
      MIT License
      •0•5•0•0•Updated May 9, 2024May 9, 2024

    • mpileup2stats

      Public
      From samtools mpileup to stats of coverage, ref_nuc, mismatches, deletions, insertions, RT-stops
      Perl
      •
      MIT License
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • modPhred

      Public
      modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
      nanoporednarnafast5on-the-flymodificationsbasecallingguppy
      Python
      •
      MIT License
      •1•16•3•0•Updated Apr 29, 2024Apr 29, 2024

    • Nm_Nanopore_Drosophila

      Public
      Detection of Nm sites from Nanopore DRS data
      R
      •0•2•0•0•Updated Mar 27, 2024Mar 27, 2024

    • DRS_CHIKV_Analysis

      Public
      Direct RNA sequencing (DRS) analysis included in article: N6-methyladenosine modification is not a general trait of viral RNA genomes
      Shell
      •0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • RPL3L

      Public
      Scripts used to produce plots in the RPL3L manuscript
      HTML
      •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • 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 2…
      rna-modification-stoichiometrypredict-rna-modificationstombo-resquiggling
      Jupyter Notebook
      •11•24•3•0•Updated Dec 21, 2022Dec 21, 2022

    • Best_Practices_dRNAseq_analysis

      Public
      Best practices for the Analysis of Oxford Nanopore Direct RNA sequencing Data (Begik*, Lucas*, et al., bioRxiv 2020)
      R
      •1•9•1•0•Updated Dec 16, 2022Dec 16, 2022

    • tRNAmap_Hoffmann_adapted

      Public
      original hoffmann pipeline, with changes for portability
      Perl
      •0•1•0•0•Updated Dec 16, 2022Dec 16, 2022

    • RNAModMachinery

      Public
      Analyses from manuscript: Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures (Begik et al. Genome Biology 2020…
      R
      •3•2•0•0•Updated Dec 16, 2022Dec 16, 2022

    • codonAutocorrelation

      Public
      Compute codon autocorrelation from fasta CDS sequences (Novoa et al., Mol Biol Evol 2019)
      synonymous-codonscodon-covariationcodon-autocorrelation
      R
      •
      MIT License
      •5•2•0•0•Updated Dec 16, 2022Dec 16, 2022

    • yeast_RNA_Mod

      Public
      Analysis of Direct RNA Sequencing of Yeast Ribosomal RNA
      R
      •1•3•1•0•Updated Dec 16, 2022Dec 16, 2022

    • lab_website

      Public archive
      Website for NovoaLab, built by the NovoaLab team
      CSS
      •
      MIT License
      •0•0•0•0•Updated Jun 14, 2022Jun 14, 2022

    • novoalab.github.io

      Public
      0•0•0•0•Updated May 5, 2022May 5, 2022

    • tombo

      Public archive
      Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
      Python
      •
      Other
      •55•0•0•0•Updated Nov 11, 2021Nov 11, 2021

    • markdown-cheatsheet

      Public
      Markdown Cheatsheet for Github Readme.md
      MIT License
      •6.4k•0•0•0•Updated Mar 22, 2021Mar 22, 2021

    • deepTools

      Public
      Tools to process and analyze deep sequencing data.
      Python
      •
      Other
      •220•0•0•0•Updated May 2, 2020May 2, 2020