Alternatives and similar repositories for megalodon:

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

• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆276Updated last week
• nanoporetech / modkit
  A bioinformatics tool for working with modified bases
  ☆185Updated last week
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆222Updated 3 months ago
• nanoporetech / ont_fast5_api
  Oxford Nanopore Technologies fast5 API software
  ☆153Updated last year
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆303Updated 2 weeks ago
• nanoporetech / taiyaki
  Training models for basecalling Oxford Nanopore reads
  ☆115Updated 3 years ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆114Updated last month
• nanoporetech / remora
  Methylation/modified base calling separated from basecalling.
  ☆171Updated 7 months ago
• wdecoster / chopper
  ☆185Updated last month
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆210Updated 4 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆209Updated last year
• jtlovell / GENESPACE
  ☆204Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated 2 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated 2 weeks ago
• nanoporetech / tombo
  Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
  ☆233Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆137Updated 3 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 6 months ago
• TobyBaril / EarlGrey
  Earl Grey: A fully automated TE curation and annotation pipeline
  ☆166Updated 2 weeks ago
• tjiangHIT / cuteSV
  Long read based human genomic structural variation detection with cuteSV
  ☆260Updated 2 weeks ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆184Updated 11 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆241Updated last year
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆160Updated last year
• rrwick / Badread
  a long read simulator that can imitate many types of read problems
  ☆212Updated 9 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆376Updated last week
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆149Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆249Updated last week
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• epi2me-labs / wf-transcriptomes
  ☆91Updated last week