Alternatives and similar repositories for deepsignal

Users that are interested in deepsignal are comparing it to the libraries listed below

• nanoporetech / tombo

  View on GitHub
  Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
  ☆234May 4, 2023Updated 2 years ago
• PengNi / deepsignal2

  View on GitHub
  ☆29Oct 17, 2023Updated 2 years ago
• WGLab / DeepMod

  View on GitHub
  DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
  ☆104Mar 8, 2023Updated 2 years ago
• nanoporetech / megalodon

  View on GitHub
  Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by a…
  ☆205May 4, 2023Updated 2 years ago
• a-slide / pycoMeth

  View on GitHub
  DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
  ☆34Feb 25, 2021Updated 4 years ago
• wdecoster / methplotlib

  View on GitHub
  Plotting tools for nanopore methylation data
  ☆94Jul 28, 2025Updated 6 months ago
• al-mcintyre / mCaller

  View on GitHub
  A python program to call methylation (m6A in DNA) from nanopore signal data
  ☆47Jun 24, 2021Updated 4 years ago
• vahidAK / NanoMethPhase

  View on GitHub
  Methylation Phasing for Nanopore Sequencing
  ☆49Mar 5, 2023Updated 2 years ago
• jts / nanopolish

  View on GitHub
  Signal-level algorithms for MinION data
  ☆594Aug 5, 2023Updated 2 years ago
• nanoporetech / rerio

  View on GitHub
  Research release basecalling models and configurations
  ☆117May 21, 2025Updated 8 months ago
• comprna / METEORE

  View on GitHub
  Automatic DNA methylation detection from nanopore tools and their consensus model
  ☆79May 22, 2023Updated 2 years ago
• PMBio / pycoMeth

  View on GitHub
  DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
  ☆30Jul 3, 2023Updated 2 years ago
• hasindu2008 / f5c

  View on GitHub
  Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
  ☆161Jan 29, 2026Updated 2 weeks ago
• Psy-Fer / SquiggleKit

  View on GitHub
  SquiggleKit: A toolkit for manipulating nanopore signal data
  ☆128Feb 16, 2024Updated last year
• nanoporetech / flappie

  View on GitHub
  Flip-flop basecaller for Oxford Nanopore reads
  ☆99Jan 13, 2022Updated 4 years ago
• novoalab / EpiNano

  View on GitHub
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆118Jul 8, 2025Updated 7 months ago
• nanoporetech / ont_fast5_api

  View on GitHub
  Oxford Nanopore Technologies fast5 API software
  ☆154Feb 27, 2024Updated last year
• nanoporetech / taiyaki

  View on GitHub
  Training models for basecalling Oxford Nanopore reads
  ☆115Jan 13, 2022Updated 4 years ago
• nanoporetech / remora

  View on GitHub
  Methylation/modified base calling separated from basecalling.
  ☆182Sep 17, 2024Updated last year
• ArtRand / signalAlign

  View on GitHub
  HMM-HDP models for MinION signal alignments
  ☆46Apr 10, 2017Updated 8 years ago
• WGLab / NanoMod

  View on GitHub
  NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
  ☆38Feb 2, 2022Updated 4 years ago
• nanoporetech / medaka

  View on GitHub
  Sequence correction provided by ONT Research
  ☆499Dec 8, 2025Updated 2 months ago
• timplab / nanopore-methylation-utilities

  View on GitHub
  ☆30Feb 5, 2021Updated 5 years ago
• nanoporetech / fast5mod

  View on GitHub
  Extract modifed base call information from Guppy Fast5 files.
  ☆14Mar 28, 2022Updated 3 years ago
• MeHelmy / princess

  View on GitHub
  ☆84Mar 3, 2025Updated 11 months ago
• nanoporetech / vbz_compression

  View on GitHub
  VBZ compression plugin for nanopore signal data
  ☆43Apr 7, 2025Updated 10 months ago
• PengNi / deepsignal-plant

  View on GitHub
  Detecting methylation using signal-level features from Nanopore sequencing reads of plants
  ☆64Jan 11, 2026Updated last month
• timplab / nanoNOMe

  View on GitHub
  nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis
  ☆20Nov 18, 2022Updated 3 years ago
• HKU-BAL / Clair

  View on GitHub
  Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
  ☆105Sep 1, 2022Updated 3 years ago
• giesselmann / nanopype

  View on GitHub
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Feb 2, 2022Updated 4 years ago
• LabShengLi / nanome

  View on GitHub
  NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)
  ☆34Dec 5, 2025Updated 2 months ago
• nanoporetech / bonito

  View on GitHub
  A PyTorch Basecaller for Oxford Nanopore Reads
  ☆428Jan 14, 2026Updated 3 weeks ago
• haotianteng / BoostNano

  View on GitHub
  A segmentation toolkit for segment the Nanopore RNA signal.
  ☆20Feb 18, 2025Updated 11 months ago
• fritzsedlazeck / Sniffles

  View on GitHub
  Structural variation caller using third generation sequencing
  ☆634Dec 18, 2025Updated last month
• nanoporetech / scrappie

  View on GitHub
  Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
  ☆93Jan 13, 2022Updated 4 years ago
• tleonardi / nanocompore

  View on GitHub
  RNA modifications detection from Nanopore dRNA-Seq data
  ☆88Jan 13, 2026Updated last month
• LooseLab / readfish

  View on GitHub
  CLI tool for flexible and fast adaptive sampling on ONT sequencers
  ☆194Apr 28, 2025Updated 9 months ago
• WGLab / NanoCaller

  View on GitHub
  Variant calling tool for long-read sequencing data
  ☆117Mar 19, 2025Updated 10 months ago
• philres / ngmlr

  View on GitHub
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆307Mar 18, 2024Updated last year