Repositories list

• CAESAR

  Public
  Python

  •0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

• PPanGGOLiN

  Public
  Build a partitioned pangenome graph from microbial genomes

  bioinformaticsmicrobial-genomicsmicrobiology+ 3comparative-genomicsbacteriapangenome

  Python

  •

  Other

  •30•289•11•1•Updated Dec 17, 2025Dec 17, 2025

• microscope-user-doc

  Public
  MicroScope Platform User Documentation

  microscope-platform

  6•3•0•0•Updated Dec 11, 2025Dec 11, 2025

• PANORAMA

  Public
  PANORAMA Project

  bioinformaticsmicrobial-genomicsmicrobiology+ 3comparative-genomicsbacteriapangenome

  Python

  •

  Other

  •0•2•0•2•Updated Dec 10, 2025Dec 10, 2025

• PANORAMA_article

  Public
  A jupyter-book corresponding to PANORAMA publication.

  Jupyter Notebook

  •1•2•0•0•Updated Dec 10, 2025Dec 10, 2025

• PanGBank-tutorial

  Public
  Some tutorials for PanGBank

  Jupyter Notebook

  •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

• netsyn

  Public
  NetSyn is a tool to detect conserved genomic contexts (i.e. synteny conservation) among a list of protein targets.

  Python

  •

  Other

  •2•8•0•0•Updated Nov 27, 2025Nov 27, 2025

• PanGBank-api

  Public
  Python

  •

  Other

  •0•0•0•1•Updated Nov 19, 2025Nov 19, 2025

• PanGBank-cli

  Public
  Command-line tool for retrieving pangenomes using the PanGBank API.

  bioinformaticsdatabasegenomics+ 3comparative-genomicspangenomeprokaryotes

  Python

  •

  Other

  •1•1•0•1•Updated Nov 19, 2025Nov 19, 2025

• metacoco

  Public
  METAbolism COmpletion for microbial COmmunities

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

• PANORAMA_test

  Public
  Dataset repository for PANORAMA GitHub test workflow

  Other

  •0•0•0•0•Updated Oct 3, 2025Oct 3, 2025

• PanGBank-wf

  Public
  A pipeline to build a PPanGGoLiN pangenome database from any source of genomes.

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

• ASMC

  Public
  ASMC is a precision tool for deciphering the amino acid diversity that composes the active site of a given homologous protein family.

  Python

  •

  Other

  •2•6•0•0•Updated Apr 3, 2025Apr 3, 2025

• PanGBank-test-datasets

  Public
  Test data to be used for automated testing with the pangbank pipeline.

  0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• asmc_2016

  Public
  ASMC code from de Melo-Minardi et al. (2010) [doi: 10.1093/bioinformatics/btq595], updated in 2016.

  Shell

  •

  Other

  •0•0•0•0•Updated Apr 16, 2024Apr 16, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.7k•0•0•0•Updated Feb 13, 2023Feb 13, 2023

• phigaro

  Public
  Phigaro is a scalable command-line tool for predicting phages and prophages

  HTML

  •

  MIT License

  •15•0•0•0•Updated Apr 28, 2022Apr 28, 2022

• PlaScope

  Public
  🔬 ⭕ Plasmid exploration of bacterial genomes

  Roff

  •

  GNU General Public License v3.0

  •4•23•3•1•Updated Mar 2, 2022Mar 2, 2022

• pangenomeNEM

  Public
  bioinformaticsmicrobiologycomparative-genomics

  C

  •

  Other

  •0•4•6•1•Updated Dec 17, 2021Dec 17, 2021

• tenacity

  Public
  Retrying library for Python

  Python

  •

  Apache License 2.0

  •305•1•0•0•Updated Mar 18, 2021Mar 18, 2021