Tool	Description	Availability
CfNano	Deconvolute cell types from cell-free DNA methylation	https://github.com/methylgrammarlab/cfdna-ont
CHEUI	Identification of m6A and m5C RNA modifications at single-molecule resolution from Nanopore sequencing	https://github.com/comprna/CHEUI-public
DeepMod	Detection of base modifications in ONT data	https://github.com/WGLab/DeepMod
DeepMP	DNA base modifications on Nanopore sequencing data	https://github.com/pepebonet/DeepMP
DeepSignal-Plant	Detecting DNA methylation state from Oxford Nanopore sequencing reads of plants	https://github.com/PengNi/deepsignal-plant
DENA	training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA	https://github.com/weir12/DENA
Differr	Detecting modifications from Nanopore direct RNA-sequencing errors using a low modification control	https://github.com/bartongroup/differr_nanopore_DRS
DNAModAnnot	R toolbox for DNA modification filtering and annotation	https://github.com/AlexisHardy/DNAModAnnot
DRUMMER	Identify RNA modifications at the nucleotide-level resolution on distinct transcript isoforms through the comparative analysis of basecall errors in Nanopore direct RNA sequencing (DRS) datasets.	https://github.com/DepledgeLab/DRUMMER
EpiNano	Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads	https://github.com/enovoa/EpiNano
F5c	A faster implementation of Nanopolish call-methylation in C	https://github.com/hasindu2008/f5c
Fast5Mod	A set of two programs for converting Guppy’s modified base Fast5 output into an aligned or unaligned BAM formatted file, and for aggregating modified base calls	https://github.com/nanoporetech/fast5mod
Haplotyped-Methylome	Using long-read sequencing to detect imprinted DNA methylation	https://github.com/scottgigante/haplotyped-methylome
MCaller	A binary classifier to improve bacterial base modification N6-methyladenine (m6a) classification by marking adenines as methylated or unmethylated based on differences between measured and expected current values as each adenine travels through the nanopore.	https://github.com/al-mcintyre/mCaller
Megalodon	Anchors raw nanopore signal to reference to call SNP and modified bases	https://github.com/nanoporetech/megalodon
MeMoRe	Methylation Motif Refiner. This is a tool designed to validate and, if necessary, refine methylation motifs detected from Bacteria and Archaea with SMRT and ONT sequencing.	https://github.com/fanglab/MeMoRe
METEORE	MEthylation deTEction with nanopORE sequencing. Automatic DNA methylation detection from nanopore tools and their consensus model	https://github.com/comprna/METEORE
MethBERT	Tool for nanopore 5mC/6 mA detection	https://github.com/yaozhong/methBERT
Methylartist	Tools for parsing and plotting methylation patterns from nanopore data	https://github.com/adamewing/methylartist
Nanocompore	A tool that identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples	https://github.com/tleonardi/nanocompore
Remora	Methylation/modified base calling separated from basecalling	https://github.com/nanoporetech/remora
SignalAlign	This paper presents one of the first methods able to detect methylation changes directly from Oxford Nanopore long-read sequencing.	https://github.com/ArtRand/signalAlign
Tombo	A suite of tools primarily for the identification of modified nucleotides	https://github.com/nanoporetech/tombo