A new section for microbial genomes has also been added, these tools may not scale to large genomes.
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- Important blog posts
- Pangenome construction
- Pangenome construction with De Bruijn graphs
- Pangenome pipelines
- Annotating pangenomes
- Short read alignment to a pangenome graph
- Long read alignment to a pangenome graph
- SNP and Structural Variant callers and genotypers
- Transcriptome analysis
- Methylation analysis
- Pangenome viewers -interactive
- Pangenome viewers -static
- Graph analysis and quality assessment
- Graph validation tools
- Pangenome comparison
- Pangenome tools for microbes
- File formats
- Miscellaneous tools
- Libraries to explore pangenomes
- Tutorials
- Other lists of pangenome tools
- Untangling-graphical-pangenomics Excellent blog by Erik Garrison explaining the differences between rGFA and GFA formats and approaches - important and frequently overlooked
- odgi Fast toolkit based on odgi format 🚀
- vg Full featured construction, mapping and SNP calling toolkit based on multiple formats. 🚀
- gaftools Toolkit for GAF (Graph Alignment Format) sorting and manipulation.
- gfakluge Toolkit and c++ API for GFA manipulation
- gfatools Toolkit for GFA parsing and conversion
- gretl (paper) Statistics and analysis for GFA files, written in Rust
- pgr-tk A PanGenomic Research Toolkit, output of this process is not a GFA file.
- GraSuite A suite of tools for GFA pangenomes and graph manipulation and pangenome.
- Minigraph (paper) Fast method by Heng Li, produces referenceGFA (rGFA) format (not GFA or odgi) 🚀
- minigraph_cactus and docs (paper) Pangenome builder which prioritizes downstream compatibility. Produces GFA and odgi. 🚀
- PGGB (paper) Pangenome Graph Builder, calculates SNPs as part of the pipeline. Produces GFA and odgi. 🚀
- pangene (paper) Pangene constructs a pangenome gene graph from one protein set and many genomes and includes simple but effective visualization 🚀
- Pantools v3+ (paper) Fully featured construction of pangenome graphs
- PSVCP (paper) Add PAV to the linear genome to construct a pangenome.
- PHG Practical Haplotype Graph (paper)
- PATO (paper) R package for pangenome construction
- Chrom_mini_graph (poster) Generate and map reads onto a coloured minimizer pangenome graph
- GET_PANGENES (paper) Perl scripts used by the Ensembl Plants team for pangenomics
- impg Create an implicit pangenome graph for a homologous target region, then use output bed files to extract sequences for PGGB etc.
- MGRgraph (preprint) An algorithm to Build a Multi-genome Reference (warning - last updated 2018)
- MEMO (preprint) MEMO constructs a pangenome and index and allows kmer based conservation analyses and visualization
- poasta Fast, gap-affine sequence-to-graph and partial order aligner and MSA construction
- SEQWISH (paper) Unbiased pangenome graphs
- seqrush Parallel pangenome construction using a simplified seqwish like algorithm.
- pannagram (preprint) Construct pangenomes and find SVs using blast, mafft and R tools
- pandagma Calculate pan-gene sets from a collection of genome assemblies and their annotations
- Panscan Construct a matrix and identify novel sequences, SVs, and repetitive regions. Requires Gencode GFF3s. Human orientated.
- CoreDetector (paper) CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes
- PanKmer (paper) PanKmer: k-mer-based and reference-free pangenome analysis
- Panaln Pangenome construction and read alignment
- AlfaPang (paper) alignment free algorithm for pangenome graph construction
- Bifrost (paper) Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
- TwoPaCo (paper) TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
- Nexus (paper) Pan-genome de Bruijn graph using the bidirectional FM-index
- Graphite (paper) Graphite: painting genomes using a colored de Bruijn graph
- nf-core pangenome (paper) A scalable Nextflow approach to building pangenomes with PGGB with visualization by odgi. 🚀
- pangepop A snakemake pipeline to create a pangenome with minigraph-cactus and align reads against it with vg giraffe
- GrAnnoT (preprint) Transfer linear genomic annotations through a pangenome GFA graph
- Annotation_scripts (preprint) Annotate a minigraph-cactus pangenome with regions or SNPs
- vg giraffe Faster and more modern alternative to vg map 🚀
- vg map Original vg mapper (superseded by vg giraffe)
- Hisat2
- Minigraph Construct graphs or align short or long reads to graphs
- Chrom_mini_graph Generate and map reads onto a coloured minimizer pangenome graph
- Panaln Pangenome construction and read alignment
- GraphAligner Fast long read graph aligner 🚀
- vg giraffe Vg giraffe can now align long reads to graphs as well
- Minigraph Construct graphs or align short or long reads to graphs
- GraphChainer Built on codebase of GraphAligner
- Spades Pathracer Align long reads to genomic graphs
- Minichain Align long reads to pangenomes in GFA or rGFA format
- PanAligner Align long reads to pangenomes
- poasta Fast, gap-affine sequence-to-graph and partial order aligner and MSA construction
- PALSS (preprint) Pangenome Graph Augmentation from Long-reads Specific Strings
- vg call Variant caller for pangenomes, with gam or GAF output 🚀
- vg surject surject to linear reference, then use linear SNP caller like Freebayes, Deepvariant etc 🚀
- Paragraph A suite of graph-based genotyping tools for short read data
- Pangenie kmer-based SV genotyping using short reads. Intended for human only (in 2023).
- Deepvariant Case study of deep variant SNP calling on vg giraffe aligned bam files
- Varigraph (preprint) A pangenome graph based genotyper for diploid and polyploid genomes
- GraphTyper A graph SV genotyper (does not call SVs)
- SVarp Use long reads to detect structural variants in a GFA format pangenome.
- bubblegun A tool for detecting Bubbles and Superbubbles
- PHI Pangenome-based Haplotype Inference (preprint) A genotyper using low coverage short or long reads for haploid pangenomes, requires Gurobi license.
- Ctyper Allele-specific and copy number specific genotyping using pangenomes
- rs-gfa-utils Rust utils for GFA format operations including ultrabubble (SV) to VCF, GAF to PAF, subgraphs etc
- BayesTyper (paper) Accurate genotyping across variant classes and lengths using variant graphs
- Swave (preprint) Detect SVs from a (minigraph) pangenome graph (free for non-commercial use)
- APAV (paper) A pangenome PAV detection and visualization toolkit in Perl and R.
- PangenomeX (paper) Pangenome shallow CNV caller in python. Requires building and normalization.
- pantas Haplotype aware differential quantification of alternative splicing events on spliced pangenome graphs
- rpvg Infer the expression of haplotype-specific transcript paths using RNA-seq reads aligned to a spliced pangenome graph
- methylGrapher Align bisulfite reads to a pangenome GFA graph and call methylation
- Pantera Identification of transposon element families from a set of pangenomes
- GraffeTE (paper) A unified framework to analyze transposable element insertion polymorphisms using graph genomes
- Pantax Pantax attempts to provide strain level metagenomic attribution for short or long reads (but requires the licensed Gurobi optimizer)
- Bandage Visualize GFA files in an interactive standalone app 🚀
- BandageNG Fork of Bandage that allows you to select and color paths and walks in the graph
- SeqTubemap Elegant path visualization for smaller regions of a pangenome from the vg team 🚀
- MoMI-G Genome graph browser for SVs visualization. User can filter and visualize annotations and inspect SVs with read alignments over the genome graph. 🚀
- pangene Pangene can visualize one protein set mapped to x genomes to check synteny and presence/absence of genes. 🚀
- Panagram Plots k-mer conservation
- VAG Visualization of short sequence alignments in a pangenome
- Panache View linearized pangenomes
- Waragraph
- PanGraphViewer Desktop and web versions. Based on cytoscape.js. Can get to chromosome coordinates, allows VCF input.
- Wally View GFA (Work in progress 2023)
- VRPG View rGFA or GFA, written in python and html
- Pantograph is a commercial pangenome graph viewer option
- PGV A web based viewer similar to SeqTubeMap
- Pancat Scripts to filter and visualize GFA files
- gfaestus GFA visualizer, GPU-accelerated using Vulkan
- gfaviz Graphical interactive tool for the visualization of sequence graphs in GFA format
- AGB Interactive assembly graph browser
- graphgenomeviewer Web based viewer for small to medium GFA files
- JBrowse 2 Web based genome browser with synteny views and plugins for multiple-alignments that can be extracted from Cactus graphs. GitHub
- strangepg A modern GFA viewer and alternative to the Bandage tool
- PG-SCunK (preprint) - assess graph representation quality using unique kmers from source genomes
- Panacus (paper) Panacus: fast and exact pangenome growth and core size estimation
- Pansel) Find overdiverse or underdiverse regions in a GFA pangenome.
- junctions Pangenome comparison using elastic-degenerate strings.
- rs-pancat-compare Pairwise pangenome graph comparison by the computation of a segmentation edit distance.
- anvi'o Microbial pangenomics - Annotation, Construction, Visualization and Manipulation (Eukaryote too excepted annotation)
- Roary A well-documented and feature-rich tool which works on Prokka gff files and has an entertaining FAQ.
- GFA An assembly interchange format read by both vg and odgi 🚀
- odgi Easy interconversion to main interchange format GFA. 🚀
- rGFA An extended GFA format, rGFA contains extra tags and includes a reference sequence. See minigraph.
- vg Vg has its own mass of file formats: https://github.com/vgteam/vg/wiki/File-Formats#gam-graph-alignment--map-vgs-bam
- PanSN-spec A naming system for haplotypes in pangenomes.
- GAF - Graph Alignment Format Created by minigraph, convertible by vg. Similar to PAF.
- GAM - Graph Alignment/Map and here Created by vg giraffe. May be superseded by GAF format.
- gfainject 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 GRAph-based Finding of Individual Motif Occurrences using vg.
- rs-gfa A GFA parser in Rust.
- rs-gfa-utils Rust utils for GFA format operations including ultrabubble (SV) to VCF, GAF to PAF, subgraphs etc
- ropebwt3 Can construct and align sequences against huge TB scale references and retrieve haplotypes.
- pollen A nascent project to develop faster tools for pangenomics in python and Rust. Contains MyGFA, FlatGFA and slow_odgi.
- mumemto Use maximal unique matches to analyze and statically visualize a set of fasta sequences.
- gfa2bin Convert various pangenome formats to Plink format for GWAS
- gfapy implements GFA1 and GFA2 parsing and scalable exploration of graphs in Python.
- gfagraphs implements rGFA and GFA1 parsing and editing of graphs in Python.
- graphanalyzer a python package to read and analyze the PAF and the GFA files for the graphs.
- INRA_pangenomes:tutorial 2024 - Nice pangenome glossary and tutorial
- Practical Pangenome Graphs
- awesome-genome-visualization - specifically tools tagged with Graph and or Pangenome
Is something missing? Contributions are welcome, please make PRs to main or write an issue with a link.