Alternatives and similar repositories for pangenie:

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

• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆114Updated last month
• colindaven / awesome-pangenomes
  A list of software for pangenomics
  ☆106Updated 2 weeks ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆111Updated 3 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆113Updated 3 months ago
• marschall-lab / panacus
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆99Updated last week
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆112Updated 6 months ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆183Updated 8 months ago
• PacificBiosciences / pb-CpG-tools
  Collection of tools for the analysis of CpG data
  ☆80Updated last month
• twolinin / longphase
  ☆109Updated 3 weeks ago
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆117Updated 2 weeks ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆140Updated 3 weeks ago
• KolmogorovLab / hapdup
  Pipeline to convert a haploid assembly into diploid
  ☆100Updated 2 months ago
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆124Updated 7 months ago
• CSU-KangHu / HiTE
  High-precision TE Annotator
  ☆103Updated 2 weeks ago
• lh3 / yak
  Yet another k-mer analyzer
  ☆131Updated 11 months ago
• asl / BandageNG
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆122Updated 3 weeks ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆96Updated last year
• HuiyangYu / PanDepth
  An ultra-fast and efficient genomic tool for coverage calculation
  ☆142Updated 7 months ago
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆109Updated 3 months ago
• marbl / ModDotPlot
  ☆138Updated this week
• ArimaGenomics / mapping_pipeline
  Mapping pipeline for data generated using Arima-HiC
  ☆76Updated 10 months ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆96Updated last year
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆91Updated 4 years ago
• wdecoster / cramino
  A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
  ☆142Updated last week
• starskyzheng / panpop
  Application of pan-genome for population
  ☆103Updated 5 months ago
• tbenavi1 / genomescope2.0
  Reference-free profiling of polyploid genomes
  ☆114Updated 8 months ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆107Updated 9 months ago
• YaoZhou89 / TGG
  tomato graph pangenome
  ☆81Updated 2 years ago
• sheinasim-USDA / HiFiAdapterFilt
  Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
  ☆86Updated 8 months ago
• c-zhou / yahs
  Yet another Hi-C scaffolding tool
  ☆142Updated 4 months ago