GeneDx/pgr-tk external links

---

GitHub - View repository

GitHub.dev - Open in online code editor

Star history - Growth chart over time

deps.dev - Dependencies and security vulnerabilities

Gitingest - Export source code for LLM usage

Repomix - Export source code for LLM usage

uithub - Export source code for LLM usage

Close

GeneDx/pgr-tk

Readme badge preview -

If you own this repo, copy the snippet below and add it to your README.md

---

Copy

[![RelatedRepos](https://img.shields.io/badge/related-repos-yellow)](https://relatedrepos.com/gh/GeneDx/pgr-tk)

Close

GeneDx / pgr-tkView on GitHubMore

• External links
• Readme badge

☆101Apr 22, 2024Updated last year

Alternatives and similar repositories for pgr-tk

Users that are interested in pgr-tk are comparing it to the libraries listed below

• pangenome / impg

  View on GitHub
  implicit pangenome graph
  ☆89Updated this week
• mlin / gfabase

  View on GitHub
  GFA insert into GenomicSQLite
  ☆49Jun 7, 2021Updated 4 years ago
• GeneDx / pgr-tk-notebooks

  View on GitHub
  ☆16Mar 17, 2023Updated 2 years ago
• codialab / panacus

  View on GitHub
  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
  ☆119Feb 3, 2026Updated 3 weeks ago
• codialab / GFAffix

  View on GitHub
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆37May 29, 2025Updated 9 months ago
• pangenome / seqwish

  View on GitHub
  alignment to variation graph inducer
  ☆157Updated this week
• waveygang / wfmash

  View on GitHub
  base-accurate DNA sequence alignments using WFA and mashmap3
  ☆210Jan 30, 2026Updated last month
• eblerjana / pangenie

  View on GitHub
  Pangenome-based genome inference
  ☆156Dec 1, 2025Updated 3 months ago
• chfi / gfaestus

  View on GitHub
  GFA visualizer, GPU-accelerated using Vulkan
  ☆76Aug 2, 2022Updated 3 years ago
• refresh-bio / agc

  View on GitHub
  Assembled Genomes Compressor
  ☆178Nov 25, 2024Updated last year
• pangenome / gfagino

  View on GitHub
  your friendly pangenome graph genotyper
  ☆10Feb 6, 2023Updated 3 years ago
• pangenome / gafpack

  View on GitHub
  convert variation graph alignments to coverage maps over nodes
  ☆27Jan 21, 2026Updated last month
• ACEnglish / kanpig

  View on GitHub
  Kmer Analysis of Pileups for Genotyping
  ☆36Jan 30, 2026Updated last month
• cschin / pgr-tk

  View on GitHub
  PGR-TK: Pangenome Research Tool Kit
  ☆21Mar 13, 2025Updated 11 months ago
• MoinSebi / gretl

  View on GitHub
  Statistics and analysis for variation graphs
  ☆49Dec 17, 2024Updated last year
• at-cg / PanAligner

  View on GitHub
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆40Dec 20, 2023Updated 2 years ago
• pangenome / genotypify

  View on GitHub
  Genotyping lots of samples with big pangenomes
  ☆11Oct 30, 2025Updated 4 months ago
• pangenome / odgi

  View on GitHub
  Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
  ☆234Feb 10, 2026Updated 2 weeks ago
• davidebolo1993 / cosigt

  View on GitHub
  COsine SImilarity-based Genotyper using pangenomes
  ☆31Feb 13, 2026Updated 2 weeks ago
• kage-genotyper / kage

  View on GitHub
  Alignment-free genotyper for SNPs and short indels, implemented in Python.
  ☆54Mar 7, 2025Updated 11 months ago
• pangenome / vcfbub

  View on GitHub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆31Jun 12, 2025Updated 8 months ago
• TimD1 / vcfdist

  View on GitHub
  vcfdist: Accurately benchmarking phased variant calls
  ☆84Feb 23, 2026Updated last week
• maickrau / GraphAligner

  View on GitHub
  ☆285Dec 29, 2025Updated 2 months ago
• fawaz-dabbaghieh / bubble_gun

  View on GitHub
  ☆41Feb 15, 2026Updated 2 weeks ago
• pangenome / pggb

  View on GitHub
  the pangenome graph builder
  ☆480Dec 8, 2025Updated 2 months ago
• pangenome / smoothxg

  View on GitHub
  linearize and simplify variation graphs using blocked partial order alignment
  ☆60Updated this week
• lh3 / pangene

  View on GitHub
  Constructing a pangenome gene graph
  ☆204Aug 11, 2025Updated 6 months ago
• vollgerlab / rustybam

  View on GitHub
  bioinformatics toolkit in rust
  ☆98Feb 15, 2026Updated 2 weeks ago
• noamteyssier / gia

  View on GitHub
  gia: Genomic Interval Arithmetic
  ☆66Aug 21, 2024Updated last year
• codeatcg / VRPG

  View on GitHub
  an interactive visualization and interpretation framework of reference-projected pangenome graphs
  ☆37Feb 15, 2025Updated last year
• ekg / pafcheck

  View on GitHub
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆15Aug 10, 2025Updated 6 months ago
• Illumina / paragraph

  View on GitHub
  Graph realignment tools for structural variants
  ☆165Dec 8, 2022Updated 3 years ago
• at-cg / minichain

  View on GitHub
  Long-read aligner to pangenome graphs
  ☆29May 20, 2024Updated last year
• tprodanov / locityper

  View on GitHub
  Targeted genotyper for complex polymorphic genes
  ☆36Updated this week
• vgteam / sequenceTubeMap

  View on GitHub
  displays multiple genomic sequences in the form of a tube map
  ☆216Nov 12, 2025Updated 3 months ago
• ekimb / mapquik

  View on GitHub
  Efficient low-divergence mapping of long reads in minimizer space
  ☆69Oct 7, 2023Updated 2 years ago
• ggonnella / gfaviz

  View on GitHub
  Graphical interactive tool for the visualization of sequence graphs in GFA format.
  ☆73Feb 19, 2019Updated 7 years ago
• Walfred-MA / Ctyper

  View on GitHub
  Genotyping of copy number sensitive allele-specific haplotypes
  ☆27Nov 6, 2025Updated 3 months ago
• HopedWall / rs-gfatovcf

  View on GitHub
  Rust implementation of Flavia95's GFAtoVCF
  ☆16Jan 17, 2022Updated 4 years ago