Set of tools to manipulate and visualize modified base bam files

Collection of tools for the analysis of CpG data

Allele-specific alignment sorting

Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.

Methylation/modified base calling separated from basecalling.

Graph Convolution based model for de novo identification of nucleotide modifications

NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

DeepMP is a computational tool to detect DNA modifications in Nanopore sequencing data

Yet another nanopore modification comparison tool

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

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

Detection of m6A from direct RNA-Seq data

Methylation Phasing for Nanopore Sequencing

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

First version of PORE-cupine. Detecting SHAPE modification using direct RNA sequencing

RNA modification detection using Nanopore raw reads with Deep One Class classification

DRUMMER: Detection of RNA modifications in nanopore direct RNA Sequencing datasets

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

Identification of differential RNA modifications from nanopore direct RNA sequencing

(m)6A (I)dentification Using (N)anopor(E) (S)equencing

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network out…

RNA modifications detection from Nanopore dRNA-Seq data

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

Signal-level algorithms for MinION data