Repositories list

• bgfa-spec

  Public
  Specifications of the BGFA format

  Creative Commons Zero v1.0 Universal

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 11, 2026Apr 11, 2026

• pygfa

  Public
  A library to manage GFA files

  Python

  •

  MIT License

  •33 forks•77 stars•33 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• pangebin

  Public
  Extracting plasmid contigs from Pangenome graphs of bacterial isolates.

  Python

  •

  MIT License

  •00 forks•11 star•11 issue•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• pantas

  Public
  Differential quantification of alternative splicing events on spliced pangenome graphs

  Python

  •

  GNU General Public License v3.0

  •11 fork•1515 stars•22 issues•11 pull request•Updated Jan 30, 2026Jan 30, 2026

• PangeBlocks-wide

  Public
  PangeBlocks for Human Genomes

  Rust

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 21, 2026Jan 21, 2026

• forgenom_summerschool2025

  Public
  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 21, 2025Oct 21, 2025

• clib

  Public
  Package manager for the C programming language.

  C

  •

  MIT License

  •263263 forks•11 star•00 issues•00 pull requests•Updated Sep 29, 2025Sep 29, 2025

• RecGraph

  Public
  Optimal sequence-to-graph alignment with recombinations

  rustalignmentpoa+ 1

  rustalignmentpoapangenomics

  Rust

  •

  MIT License

  •33 forks•4040 stars•33 issues•00 pull requests•Updated Jul 25, 2025Jul 25, 2025

• pangebin-doc

  Public
  Clone of overleaf Pangebin V2 document

  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 4, 2025Jul 4, 2025

• cpm2025

  Public
  Combinatorial Pattern Matching 2025

  HTML

  •

  GNU General Public License v2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 23, 2025Jun 23, 2025

• rec_align_exps

  Public
  Experiments for RecAlign

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 4, 2025May 4, 2025

• complexCGR

  Public
  complex Chaos Game Representation for DNA sequences

  Python

  •

  MIT License

  •22 forks•2121 stars•00 issues•00 pull requests•Updated Apr 3, 2025Apr 3, 2025

• pgbh2025

  Public
  Pangenome Bio Hacking 2025

  Ruby

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2025Jan 22, 2025

• cancer_ea

  Public
  cancer phylogeny genetic programming

  Python

  •22 forks•22 stars•00 issues•00 pull requests•Updated Dec 5, 2024Dec 5, 2024

• pangeblocks

  Public
  pangenome from maximal blocks in an MSA

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•1111 stars•22 issues•11 pull request•Updated Sep 17, 2024Sep 17, 2024

• galig

  Public
  A graph aligner

  Python

  •

  GNU General Public License v3.0

  •1313 forks•3131 stars•88 issues•00 pull requests•Updated Sep 17, 2024Sep 17, 2024

• RecGraph-exps

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2024Jul 17, 2024

• COPA24

  Public
  PhD school on Evolution in Computational Pangenomics

  MIT License

  •8383 forks•00 stars•00 issues•00 pull requests•Updated Feb 14, 2024Feb 14, 2024

• materiale-stage-tesi

  Public
  Una raccolta di materiale utile per tutti gli studenti che iniziano a lavorare

  Rust

  •

  Creative Commons Zero v1.0 Universal

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2024Jan 31, 2024

• rs-gax

  Public
  Rust

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 2, 2023Dec 2, 2023

• ESGq

  Public
  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 1, 2023Jul 1, 2023

• meta_cancer

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 27, 2023Jun 27, 2023

• LightStringGraph

  Public
  Lightweight String Graph Construction

  C++

  •

  GNU General Public License v3.0

  •11 fork•1111 stars•00 issues•00 pull requests•Updated May 10, 2023May 10, 2023

• pangeblocks-experiments

  Public
  Experiments to evaluate graph constructions made with pangeblocks and other tools

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• Wild-pBWT

  Public
  PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards

  haplotypesbwthaplotype-blocks+ 1

  haplotypesbwthaplotype-blockspbwt

  C++

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2023Apr 3, 2023

• malva

  Public
  genotyping by Mapping-free ALternate-allele detection of known VAriants

  bioinformaticsngsvcf+ 2

  bioinformaticsngsvcfalignment-freegenotyping

  C

  •

  GNU General Public License v3.0

  •44 forks•1010 stars•33 issues•00 pull requests•Updated Mar 6, 2023Mar 6, 2023

• deap

  Public
  Distributed Evolutionary Algorithms in Python

  Python

  •

  GNU Lesser General Public License v3.0

  •1.2k1.2k forks•11 star•00 issues•00 pull requests•Updated Feb 8, 2023Feb 8, 2023

• MALVIRUS

  Public
  A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)

  kmeralignment-freevirology+ 3

  kmeralignment-freevirologygenotyping-by-sequencinggenotypingsars-cov-2

  JavaScript

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• CouGaR-g

  Public
  Frequence Chaos Game Representation of DNA with Deep Learning

  Python

  •

  GNU General Public License v3.0

  •55 forks•55 stars•00 issues•00 pull requests•Updated Sep 25, 2022Sep 25, 2022

• rs-vgaligner

  Public
  Rust implementation of ekg's dozyg

  rustbioinformaticsanchors+ 4

  rustbioinformaticsanchorsalignmentkmerpoachaining

  Rust

  •

  MIT License

  •00 forks•99 stars•00 issues•00 pull requests•Updated Jun 27, 2022Jun 27, 2022