Alternatives and similar repositories for deepsignal-plant

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

• PengNi / deepsignal2

  View on GitHub
  ☆29Oct 17, 2023Updated 2 years ago
• zhongzhd / ont_m6a_detection

  View on GitHub
  ☆10Mar 11, 2025Updated 11 months 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
• 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
• fritzsedlazeck / sge_mummer

  View on GitHub
  Scripts to split reference and run mummer in parallel on an SGE cluster
  ☆11Oct 14, 2016Updated 9 years ago
• bartongroup / 2passtools

  View on GitHub
  Two pass alignment for long reads
  ☆22Mar 9, 2021Updated 4 years ago
• mkirsche / Grafter

  View on GitHub
  Scaffolding with Ultralong Reads
  ☆15Nov 11, 2020Updated 5 years ago
• bioinfomaticsCSU / deepsignal

  View on GitHub
  Detecting methylation using signal-level features from Nanopore sequencing reads
  ☆118Jun 4, 2023Updated 2 years ago
• ArtRand / signalAlign

  View on GitHub
  HMM-HDP models for MinION signal alignments
  ☆46Apr 10, 2017Updated 8 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
• gt1 / daccord

  View on GitHub
  d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly
  ☆19Sep 12, 2018Updated 7 years ago
• nanoporetech / fast5mod

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

  View on GitHub
  Yet another nanopore modification comparison tool
  ☆12Mar 4, 2022Updated 3 years ago
• PengNi / ccsmethphase

  View on GitHub
  Methylatino phasing using PacBio CCS reads
  ☆14Dec 13, 2024Updated last year
• treangenlab / methphaser

  View on GitHub
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆54Mar 5, 2025Updated 11 months ago
• pepebonet / DeepMP

  View on GitHub
  DeepMP is a computational tool to detect DNA modifications in Nanopore sequencing data
  ☆28Mar 18, 2022Updated 3 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
• mirnylab / hiclib-legacy

  View on GitHub
  A legacy repository. Was replaced by distiller, cooler, and cooltools.
  ☆21Mar 4, 2020Updated 5 years ago
• comprna / radian

  View on GitHub
  Nanopore direct RNA basecaller
  ☆11Oct 27, 2022Updated 3 years ago
• daewoooo / SaaRclust

  View on GitHub
  ☆10Mar 4, 2025Updated 11 months ago
• lh3 / dipcall

  View on GitHub
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆105Jun 6, 2021Updated 4 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
• hiruna72 / squigualiser

  View on GitHub
  Visualise and analyse nanopore (ONT) raw signals
  ☆128Dec 12, 2025Updated 2 months ago
• BilkentCompGen / hercules

  View on GitHub
  Profile HMM-based hybrid error correction algorithm for long reads
  ☆21Aug 15, 2018Updated 7 years ago
• xiaochuanle / Falign

  View on GitHub
  An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)
  ☆14Oct 23, 2024Updated last year
• imsuneth / realfreq

  View on GitHub
  Realtime base modification frequency tool
  ☆13Sep 16, 2025Updated 5 months ago
• hasindu2008 / slow5lib

  View on GitHub
  slow5lib is a software library for reading & writing SLOW5 files.
  ☆47Jan 28, 2026Updated 2 weeks 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…
  ☆203May 4, 2023Updated 2 years ago
• koszullab / hicstuff

  View on GitHub
  Simple library/pipeline to generate and handle Hi-C data.
  ☆39Updated this week
• 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
• morispi / CONSENT

  View on GitHub
  Scalable long read self-correction and assembly polishing with multiple sequence alignment
  ☆54Feb 6, 2024Updated 2 years ago
• xiaochuanle / MECAT

  View on GitHub
  MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
  ☆111Oct 2, 2020Updated 5 years ago
• ekg / gimbricate

  View on GitHub
  recompute GFA link overlaps
  ☆25Sep 14, 2022Updated 3 years ago
• nanoporetech / pomfret

  View on GitHub
  ☆27Nov 14, 2025Updated 3 months ago
• giesselmann / nanopype

  View on GitHub
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Feb 2, 2022Updated 4 years ago
• xiaochuanle / MECAT2

  View on GitHub
  ☆71Apr 28, 2020Updated 5 years ago
• gaoyubang / nanom6A

  View on GitHub
  ☆24Dec 24, 2022Updated 3 years ago
• pangenome / vcfbub

  View on GitHub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆31Jun 12, 2025Updated 8 months ago
• nanoporetech / vbz_compression

  View on GitHub
  VBZ compression plugin for nanopore signal data
  ☆43Apr 7, 2025Updated 10 months ago