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
  ☆258Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆203Updated 3 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆181Updated 2 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆135Updated 3 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆261Updated 2 weeks ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆274Updated 4 months ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆113Updated 7 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆207Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆141Updated last year
• nanoporetech / modkit
  A bioinformatics tool for working with modified bases
  ☆171Updated this week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆242Updated 3 months ago
• nanoporetech / ont_fast5_api
  Oxford Nanopore Technologies fast5 API software
  ☆152Updated 11 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆107Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆296Updated last week
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆157Updated last year
• nanoporetech / taiyaki
  Training models for basecalling Oxford Nanopore reads
  ☆115Updated 3 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆217Updated last month
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆371Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆198Updated 2 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆219Updated 4 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆192Updated 3 weeks ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆207Updated last year
• epi2me-labs / wf-transcriptomes
  ☆86Updated last month
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆319Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆203Updated 2 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆233Updated last year
• wdecoster / chopper
  ☆171Updated last week