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
- 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 Statistics and analysis for GFA files, written in Rust
- pgr-tk A PanGenomic Research Took Kit, output of this process is not a GFA file.
- Minigraph Fast method by Heng Li, produces referenceGFA (rGFA) format (not GFA or odgi) 🚀
- minigraph_cactus and docs Pangenome builder which prioritizes downstream compatibility. Produces GFA and odgi. 🚀
- PGGB Pangenome Graph Builder, calculates SNPs as part of the pipeline. Produces GFA and odgi. 🚀
- pangene Pangene constructs a pangenome gene graph from one protein set and many genomes and includes simple but effective visualization 🚀
- Pantools v3+ Fully featured construction of pangenome graphs
- PSVCP Add PAV to the linear genome to construct a pangenome.
- PHG Practical Haplotype Graph
- PATO R package for pangenome construction
- Chrom_mini_graph Generate and map reads onto a coloured minimizer pangenome graph
- GET_PANGENES 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 An algorithm to Build a Multi-genome Reference (warning - last updated 2018)
- MEMO 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
- 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
- Annotation_scripts and 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
- GraphAligner Fast long read graph aligner 🚀
- 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
- vg call SNP 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
- vg call Call and genotype structural variants on a graph using long and short reads. 🚀
- GraphTyper A graph SV genotyper (does not call SVs)
- Pangenie kmer-based SV genotyping using short reads. Intended for human only (in 2023).
- 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.
*Pantera Identification of transposon element families from a set of pangenomes
- Bandage Visualize GFA files in an interactive standalone app 🚀
- 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 (https://github.com/cmdcolin/jbrowse-plugin-mafviewer)
- strangepg A modern GFA viewer and alternative to the Bandage tool
- 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 it's 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.
- ropebwt3 Can construct and align sequences against huge TB scale references and retrieve haplotypes.
- 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.
- 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.
