Repositories list

• 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)

  nanoporernam6a-rna-modifications

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•15•2•0•Updated Dec 16, 2024Dec 16, 2024

• SeqTagger

  Public
  Super-fast and accurate demultiplexing of direct RNA-seq runs.

  nanoporesequencingrna+ 2directdemultiplexing

  Jupyter Notebook

  •

  Other

  •1•4•1•0•Updated Dec 5, 2024Dec 5, 2024

• polyTailor

  Public
  Poly-A tail length estimation from Nano3P-seq libraries

  Jupyter Notebook

  •0•1•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•0•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•14•2•0•Updated Sep 19, 2024Sep 19, 2024

• EpiNano

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

  nanoporerna-sequencingm6a+ 2m6a-rna-modificationsdirect-rna

  Python

  •

  GNU General Public License v2.0

  •31•113•3•1•Updated Jun 30, 2024Jun 30, 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

  nanoporednarna+ 5fast5on-the-flymodificationsbasecallingguppy

  Python

  •

  MIT License

  •1•16•2•0•Updated Apr 29, 2024Apr 29, 2024

• Nm_Nanopore_Drosophila

  Public
  Detection of Nm sites from Nanopore DRS data

  R

  •0•1•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

• Nano3P_Seq

  Public
  Nanopore 3' end-capture sequencing (Begik et al., bioRxiv 2021)

  Python

  •

  MIT License

  •3•12•1•0•Updated Jul 18, 2023Jul 18, 2023

• RPL3L

  Public
  Scripts used to produce plots in the RPL3L manuscript

  HTML

  •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

• NanoConsensus

  Public
  R

  •

  MIT License

  •0•1•0•0•Updated Mar 7, 2023Mar 7, 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 2021)

  rna-modification-stoichiometrypredict-rna-modificationstombo-resquiggling

  Jupyter Notebook

  •10•23•2•1•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•0•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

  •54•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

  •212•0•0•0•Updated May 2, 2020May 2, 2020

• MasterOfPores

  Public
  Nextflow pipeline for analysis of direct RNA Nanopore reads (Cozzuto et al., Front in Genet 2020)

  HTML

  •

  MIT License

  •16•1•0•0•Updated Apr 6, 2020Apr 6, 2020

• DeePlexiCon

  Public
  Signal based nanopore RNA demultiplexing with convolutional neural networks (Smith*, Ersavas*, Ferguson* et al., Genome Research 2020)

  Jupyter Notebook

  •

  MIT License

  •8•0•0•0•Updated Jan 17, 2020Jan 17, 2020

• riboflow

  Public
  Pipeline for Ribosome Profiling Data

  Groovy

  •

  MIT License

  •9•0•0•0•Updated Dec 20, 2019Dec 20, 2019

• SquiggleKit

  Public
  SquiggleKit: A toolkit for manipulating nanopore signal data

  Python

  •

  MIT License

  •23•1•0•0•Updated Dec 2, 2019Dec 2, 2019

• differr_nanopore_DRS

  Public
  Scripts for identifying sites with differential error rates in mapped nanopore DRS data

  Python

  •3•1•0•0•Updated Aug 13, 2019Aug 13, 2019