A list of software capable of analyzing mainly eukaryotic genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes.
🚀 indicates a popular repository
(2014-2019) Heng Li's Blog: The Birth of GFA and Pangenome Models
This series of posts serves as a modern history of the core problems and solutions in pangenomics. It documents the initial proposal of the Graphical Fragment Assembly (GFA) format and outlines [...]
(2019) Untangling-graphical-pangenomics Excellent blog by Erik Garrison explaining the differences between rGFA and GFA forma[...]
(2024) On the definition of pangenome In this post, Heng Li traces the definition of "pangenome" from its 2005 bacterial origins (focused [...]
Tool
Repository
Description
Status
odgi GitHub Fast toolkit based on odgi format
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vg GitHub Full featured construction, mapping and SNP calling toolkit based on multiple formats.
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gaftools GitHub Toolkit for GAF (Graph Alignment Format) sorting and manipulation.
gfakluge GitHub Toolkit and c++ API for GFA manipulation
gfatools GitHub Toolkit for GFA parsing and conversion
gretl GitHub (paper )Statistics and analysis for GFA files, written in Rust
pgr-tk GitHub A PanGenomic Research Toolkit, output of this process is not a GFA file.
GraSuite Forge A suite of tools for GFA pangenomes and graph manipulation and pangenome.
gratools Forge (preprint )Handle GFA genomes quickly, calculate node depth and other operations
Pangenome construction with De Bruijn graphs
Tool
Repository
Description
Status
Bifrost GitHub (paper )Bifrost: highly parallel construction and indexing of colored de Bruijn graphs
TwoPaCo GitHub (paper )TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph
Nexus GitHub (paper )Pangenome de Bruijn graph construction using the bidirectional algorithm
Graphite GitHub (paper )Graphite: painting genomes using a colored de Bruijn graph
BCALM 2 GitHub (paper )State-of-the-art ultra-low memory and fast de Bruijn graph construction from sequencing data, convertible to GFA
Tool
Repository
Description
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nf-core pangenome GitHub (paper )A scalable Nextflow approach to building pangenomes with PGGB with visualization
Short read alignment to a pangenome graph Long read alignment to a pangenome graph SNP and Structural Variant callers and genotypers
Tool
Repository
Description
Status
pantas GitHub Haplotype aware differential quantification of alternative splicing events on spliced pangenome graphs
rpvg GitHub Infer the expression of haplotype-specific transcript paths using RNA-seq reads aligned to a spliced pangenome graph
PanGraphRNA GitHub (paper )A docker and galaxy based platform for graph pangenome-based RNA-seq analysis
Tool
Repository
Description
Status
methylGrapher GitHub Align bisulfite reads to a pangenome GFA graph and call methylation
Tool
Repository
Description
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Pantera GitHub Identification of transposon element families from a set of pangenomes
GraffeTE GitHub (paper )A unified framework to analyze transposable element insertion polymorphisms using graph-based methods
Tool
Repository
Description
Status
Pantax GitHub Pantax attempts to provide strain level metagenomic attribution for short or long reads (but requires the licensed Gurobi optimizer)
Pangenome viewers -interactive
Tool
Repository
Description
Status
Bandage GitHub Visualize GFA files in an interactive standalone app
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BandageNG GitHub Fork of Bandage that allows you to select and color paths and walks in the graph
SeqTubemap GitHub Elegant path visualization for smaller regions of a pangenome from the vg team
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MoMI-G GitHub Genome graph browser for SVs visualization. User can filter and visualize annotations and inspect SVs with read alignments over the genome graph.
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pangene GitHub Pangene can visualize one protein set mapped to x genomes to check synteny and presence/absence of genes.
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Panagram GitHub Alignment-free pangenome browser and analysis toolkit, can analyze and plot k-mer conservation (do not confuse with pannagram above)
VAG GitHub Visualization of short sequence alignments in a pangenome
Panache GitHub View linearized pangenomes
Waragraph GitHub Pangenome graph visualization
PanGraphViewer GitHub Desktop and web versions. Based on cytoscape.js. Can get to chromosome coordinates, allows VCF input.
Wally GitHub View GFA (Work in progress 2023)
VRPG GitHub View rGFA or GFA, written in python and html
Pantograph Web is a commercial pangenome graph viewer option
PGV GitHub A web based viewer similar to SeqTubeMap
Pancat GitHub Scripts to filter and visualize GFA files
gfaestus GitHub GFA visualizer, GPU-accelerated using Vulkan
gfaviz GitHub Graphical interactive tool for the visualization of sequence graphs in GFA format
AGB GitHub Interactive assembly graph browser
graphgenomeviewer Web Web based viewer for small to medium GFA files
JBrowse 2 GitHub / Web Web based genome browser with synteny views and plugins for multiple-alignments that can be extracted from Cactus graphs.
strangepg GitHub A modern GFA viewer and alternative to the Bandage tool
savanache Forge (preprint )A browser based viewer appropriate for GFA files from minigraph-cactus
Pangenome viewers -static
Tool
Repository
Description
Status
vg view GitHub generates static images from a vg compatible file
odgi GitHub can generate genome wide static images from an odgi or gfa file
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plotsr GitHub Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple linear genomes
gfalook GitHub A 2026 reimplementation of odgi viz in rust with more features.
Graph analysis and quality assessment
Tool
Repository
Description
Status
PG-SCunK GitHub (preprint )assess graph representation quality using unique kmers from source genomes
Panacus GitHub (paper )Panacus: fast and exact pangenome growth and core size estimation
Pansel GitHub Find overdiverse or underdiverse regions in a GFA pangenome.
Tool
Repository
Description
Status
junctions GitHub Pangenome comparison using elastic-degenerate strings.
rs-pancat-compare GitHub Pairwise pangenome graph comparison by the computation of a segmentation edit distance.
Tool
Repository
Description
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Panaroo Github (paper )Popular prokaryotic analysis pipeline for up to 10k bacterial genomes
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PPanGGOLiN GitHub (paper )Partitioned pangenome graph, scale to >10k genomes - detection of regions of genomic plasticity - precomputed pangenomes available in PanGBank .
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Panalyze GitHub (paper )Viral pangenome variation graphs - Construction, Refinement, Annotation, Visualisation, Manipulation
anvi'o Web (paper )Microbial pangenomics - Annotation, Construction, Visualization and Manipulation (can be used for eukaryotes too except for annotation)
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Roary GitHub (paper )A well-documented and feature-rich tool which works on Prokka gff files and has an entertaining FAQ.
pandora GitHub (paper )Pan-genome graph structure and algorithms for identifying variants across diverse samples
Tool
Repository
Description
Status
gfainject GitHub Map short alignments in BAM format to a GFA (seems it is not a real aligner but a conversion tool). Output in GAF format.
GRAFIMO GitHub GRAph-based Finding of Individual Motif Occurrences using vg.
rs-gfa GitHub A GFA parser in Rust.
rs-gfa-utils GitHub Rust utils for GFA format operations including ultrabubble (SV) to VCF, GAF to PAF, subgraphs etc
ropebwt3 GitHub Can construct and align sequences against huge TB scale references and retrieve haplotypes.
pollen GitHub A nascent project to develop faster tools for pangenomics in python and Rust. Contains MyGFA, FlatGFA and slow_odgi.
mumemto GitHub Use maximal unique matches to analyze and statically visualize a set of fasta sequences.
shredtools GitHub Rapidly access gene level or syntenic MUMs in a Mumemto pangenome
gfa2bin GitHub Convert various pangenome formats to Plink format for GWAS
vizitig GitLab (preprint )An all-in-one genomic and transcriptomic de Bruijn graph constructor
gafpack GitHub Calculate node coverage from GAF alignments to GFA variation graphs.
TeraTools GitHub Efficient terabase scale pangenome analysis tools for large datasets
Kente GitHub (preprint )A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbial Genomes
MSpangenome GitLab (preprint )Simulating population pangenomes under coalescent demographic models
Libraries to explore pangenomes
Library
Repository
Description
Status
gfapy GitHub Implements GFA1 and GFA2 parsing and scalable exploration of graphs in Python.
gfagraphs GitHub Implements rGFA and GFA1 parsing and editing of graphs in Python.
graphanalyzer GitHub A python package to read and analyze the PAF and the GFA files for the graphs.
theseus GitHub (preprint )A fast and optimal sequence to graph alignment library and non-greedy implementation
INRA_pangenomes:tutorial 2024 - Nice pangenome glossary and tutorialBao_2025 [ A 2025 review on pangenomics]Bocs_2026 A review of what is currently possible in pangenomics, and what tools and formats are really missing.
Is something missing? Contributions are welcome, please make PRs to main or write an issue with a link.
This is not "published" in an academic journal, but you can cite it via the Zenodo DOI at the top if you like.
