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https://github.com/colindaven/awesome-pangenomes

A list of software for pangenomics
https://github.com/colindaven/awesome-pangenomes

List: awesome-pangenomes

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A list of software for pangenomics

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# awesome-pangenomes

## 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. 



:rocket: indicates a popular repository



# Important blog posts



* [Untangling-graphical-pangenomics](https://ekg.github.io/2019/07/09/Untangling-graphical-pangenomics) Excellent blog by Erik Garrison explaining the differences between rGFA and GFA formats and approaches - *important and frequently overlooked* 



# Toolkits



* [odgi](https://github.com/pangenome/odgi) Fast toolkit based on odgi format :rocket:

* [vg](https://github.com/vgteam/vg) Full featured construction, mapping and SNP calling toolkit based on multiple formats. :rocket:

* [gaftools](https://github.com/marschall-lab/gaftools) Toolkit for GAF (Graph Alignment Format) sorting and manipulation.

* [gfakluge](https://github.com/edawson/gfakluge) Toolkit and c++ API for GFA manipulation

* [gfatools](https://github.com/lh3/gfatools) Toolkit for GFA parsing and conversion

* [gretl](https://github.com/MoinSebi/gretl) Statistics and analysis for GFA files, written in Rust

* [pgr-tk](https://github.com/GeneDx/pgr-tk) A PanGenomic Research Took Kit, output of this process is not a GFA file.



# Pangenome construction



* [Minigraph](https://github.com/lh3/minigraph) Fast method by Heng Li, produces referenceGFA (rGFA) format (not GFA or odgi) :rocket:

* [minigraph_cactus](https://github.com/ComparativeGenomicsToolkit/cactus) and [docs](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) Pangenome builder which prioritizes downstream compatibility. Produces GFA and odgi. :rocket:

* [PGGB](https://github.com/pangenome/pggb) Pangenome Graph Builder, calculates SNPs as part of the pipeline. Produces GFA and odgi. :rocket:

* [pangene](https://github.com/lh3/pangene) Pangene constructs a pangenome gene graph from one protein set and many genomes and includes simple but effective visualization :rocket:

* [Pantools v3+](https://git.wur.nl/bioinformatics/pantools) Fully featured construction of pangenome graphs

* [PSVCP](https://github.com/wjian8/psvcp_v1.01) Add PAV to the linear genome to construct a pangenome.

* [PHG Practical Haplotype Graph](https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/Home)

* [PATO](https://github.com/irycisBioinfo/PATO) R package for pangenome construction

* [Chrom_mini_graph](https://github.com/gaojunxuan/chrom_mini_graph) Generate and map reads onto a coloured minimizer pangenome graph

* [GET_PANGENES](https://github.com/Ensembl/plant-scripts/tree/master/pangenes) Perl scripts used by the Ensembl Plants team for pangenomics

* [impg](https://github.com/ekg/impg) Create an implicit pangenome graph for a homologous target region, then use output bed files to extract sequences for PGGB etc.

* [MGRgraph](https://github.com/LeilyR/Multi-genome-Reference) An algorithm to Build a Multi-genome Reference (warning - last updated 2018)

* [MEMO](https://github.com/StephenHwang/MEMO) MEMO constructs a pangenome and index and allows kmer based conservation analyses and visualization

* [poasta](https://github.com/broadinstitute/poasta) Fast, gap-affine sequence-to-graph and partial order aligner and MSA construction



# Pangenome pipelines



* [nf-core pangenome](https://github.com/nf-core/pangenome) [Paper](https://doi.org/10.1093/bioinformatics/btae609) A scalable Nextflow approach to building pangenomes with PGGB with visualization by odgi. :rocket:

* [pangepop](https://forgemia.inra.fr/pangepop/pangepop) A snakemake pipeline to create a pangenome with minigraph-cactus and align reads against it with vg giraffe



# Annotating pangenomes

* [Annotation_scripts](https://github.com/jmonlong/manu-vggafannot/tree/main/analysis) and [preprint](https://www.biorxiv.org/content/10.1101/2024.10.12.618009v1) Annotate a minigraph-cactus pangenome with regions or SNPs



# Short read alignment to a pangenome graph



* [vg giraffe](https://github.com/vgteam/vg) Faster and more modern alternative to vg map :rocket:

* [vg map](https://github.com/vgteam/vg) Original vg mapper (superseded by vg giraffe)

* [Hisat2](https://github.com/DaehwanKimLab/hisat2)

* [Minigraph](https://github.com/lh3/minigraph) Construct graphs or align short or long reads to graphs

* [Chrom_mini_graph](https://github.com/gaojunxuan/chrom_mini_graph) Generate and map reads onto a coloured minimizer pangenome graph



# Long read alignment to a pangenome graph



* [GraphAligner](https://github.com/maickrau/GraphAligner) Fast long read graph aligner :rocket:

* [Minigraph](https://github.com/lh3/minigraph) Construct graphs or align short or long reads to graphs 

* [GraphChainer](https://github.com/algbio/GraphChainer) Built on codebase of GraphAligner

* [Spades Pathracer](https://github.com/eodus/pathracer#sec4.3) Align long reads to genomic graphs

* [Minichain](https://github.com/at-cg/minichain) Align long reads to pangenomes in GFA or rGFA format

* [PanAligner](https://github.com/at-cg/PanAligner) Align long reads to pangenomes

* [poasta](https://github.com/broadinstitute/poasta) Fast, gap-affine sequence-to-graph and partial order aligner and MSA construction



# SNP callers and genotypers



* [vg call](https://github.com/vgteam/vg) SNP caller for pangenomes, with gam or GAF output :rocket:

* [vg surject](https://github.com/vgteam/vg) surject to linear reference, then use linear SNP caller like Freebayes, Deepvariant etc :rocket:

* [Paragraph](https://github.com/Illumina/paragraph) A suite of graph-based genotyping tools for short read data

* [Pangenie](https://github.com/eblerjana/pangenie) kmer-based SV genotyping using short reads. Intended for human only (in 2023).

* [Deepvariant](https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-vg-case-study.md) Case study of deep variant SNP calling on vg giraffe aligned bam files



# Structural Variation (SV) callers and genotypers



* [vg call](https://github.com/vgteam/vg) Call and genotype structural variants on a graph using long and short reads. :rocket:

* [GraphTyper](https://github.com/DecodeGenetics/graphtyper) A graph SV genotyper (does not call SVs)  

* [Pangenie](https://github.com/eblerjana/pangenie) kmer-based SV genotyping using short reads. Intended for human only (in 2023).

* [SVarp](https://github.com/asylvz/SVarp) Use long reads to detect structural variants in a GFA format pangenome.

* [bubblegun](https://github.com/fawaz-dabbaghieh/bubble_gun) A tool for detecting Bubbles and Superbubbles

* [PHI Pangenome-based Haplotype Inference](https://github.com/at-cg/PHI) [preprint](https://www.biorxiv.org/content/10.1101/2024.10.27.620212v1) A genotyper using low coverage short or long reads for haploid pangenomes, requires Gurobi license.



# Repeat analysis tools



*[Pantera](https://github.com/piosierra/pantera) Identification of transposon element families from a set of pangenomes



# Pangenome viewers -interactive



* [Bandage](https://github.com/rrwick/Bandage) Visualize GFA files in an interactive standalone app :rocket:

* [SeqTubemap](https://github.com/vgteam/sequenceTubeMap) Elegant path visualization for smaller regions of a pangenome from the vg team :rocket:

* [MoMI-G](https://github.com/MoMI-G/MoMI-G/) Genome graph browser for SVs visualization. User can filter and visualize annotations and inspect SVs with read alignments over the genome graph. :rocket:

* [pangene](https://github.com/lh3/pangene) Pangene can visualize one protein set mapped to x genomes to check synteny and presence/absence of genes. :rocket:

* [Panagram](https://github.com/kjenike/panagram) Plots k-mer conservation

* [VAG](https://github.com/lipingfangs/VAG) Visualization of short sequence alignments in a pangenome

* [Panache](https://github.com/SouthGreenPlatform/panache) View linearized pangenomes

* [Waragraph](https://github.com/chfi/waragraph)

* [PanGraphViewer](https://github.com/TF-Chan-Lab/panGraphViewer) Desktop and web versions. Based on cytoscape.js. Can get to chromosome coordinates, allows VCF input.

* [Wally](https://github.com/tobiasrausch/wally#subcommand-gfa-visualization-of-pan-genome-graphs-work-in-progress) View GFA (Work in progress 2023)

* [VRPG](https://github.com/codeatcg/VRPG) View rGFA or GFA, written in python and html

* [Pantograph](https://help.pantograph.computomics.com/) is a commercial pangenome graph viewer option

* [PGV](https://github.com/w-gao/pgv) A web based viewer similar to SeqTubeMap

* [Pancat](https://github.com/Tharos-ux/pancat) Scripts to filter and visualize GFA files

* [gfaestus](https://github.com/chfi/gfaestus) GFA visualizer, GPU-accelerated using Vulkan 

* [gfaviz](https://github.com/ggonnella/gfaviz) Graphical interactive tool for the visualization of sequence graphs in GFA format

* [AGB](https://github.com/almiheenko/AGB) Interactive assembly graph browser

* [graphgenomeviewer](https://cmdcolin.github.io/graphgenomeviewer/) Web based viewer for small to medium GFA files

* [JBrowse 2](https://jbrowse.org) 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](https://github.com/qwx9/strangepg) A modern GFA viewer and alternative to the Bandage tool



# Pangenome viewers -static



* [vg view](https://github.com/vgteam/vg) - generates static images

* [odgi](https://github.com/pangenome/odgi) - generates static images :rocket:

* [plotsr](https://github.com/schneebergerlab/plotsr) - generates static images



# Graph validation tools



* [vg validate](https://github.com/vgteam/vg)

* [odgi validate](https://github.com/pangenome/odgi)



# Pangenome comparison



* [junctions](https://github.com/urbanslug/junctions) Pangenome comparison using elastic-degenerate strings.

* [rs-pancat-compare](https://github.com/dubssieg/rs-pancat-compare) Pairwise pangenome graph comparison by the computation of a segmentation edit distance.



# Pangenome tools for microbes



* [anvi'o](https://merenlab.org/2016/11/08/pangenomics-v2/) Microbial pangenomics - Annotation, Construction, Visualization and Manipulation (Eukaryote too excepted annotation)

* [Roary](https://github.com/sanger-pathogens/Roary) A well-documented and feature-rich tool which works on Prokka gff files and has an entertaining FAQ. 



# File formats



* [GFA](http://gfa-spec.github.io/GFA-spec/GFA1.html) An assembly interchange format read by both vg and odgi :rocket:

* [odgi](https://github.com/pangenome/odgi) Easy interconversion to main interchange format GFA. :rocket:

* [rGFA](https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) An extended GFA format, rGFA contains extra tags and includes a reference sequence. See minigraph.

* [vg](https://github.com/vgteam/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](https://github.com/pangenome/PanSN-spec) A naming system for haplotypes in pangenomes

* [GAF - Graph Alignment Format](https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-graph-alignment-format-gaf) Created by minigraph, convertible by vg. Similar to PAF.

* [GAM - Graph Alignment/Map](https://github.com/vgteam/vg/wiki/File-Formats#gam-graph-alignment--map-vgs-bam) and [here](https://github.com/vgteam/libvgio/blob/master/deps/vg.proto#L38-L54) Created by vg giraffe. May be superseded by GAF format.



# Miscellaneous tools



* [gfainject](https://github.com/chfi/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](https://github.com/pinellolab/GRAFIMO) GRAph-based Finding of Individual Motif Occurrences using vg

* [rs-gfa](https://github.com/chfi/rs-gfa) A GFA parser in Rust.

* [ropebwt3](https://github.com/lh3/ropebwt3) Can construct and align sequences against huge TB scale references and retrieve haplotypes.



# kmer based approaches



* [PanKmer](https://gitlab.com/salk-tm/pankmer)



# Libraries to explore pangenomes



* [gfapy](https://github.com/ggonnella/gfapy) implements GFA1 and GFA2 parsing and scalable exploration of graphs in Python

* [gfagraphs](https://github.com/Tharos-ux/gfagraphs) implements rGFA and GFA1 parsing and editing of graphs in Python

* [graphanalyzer](https://github.com/sablokgaurav/graphanalyzer) a python package to read and analyze the PAF and the GFA files for the graphs.



# Other lists of pangenome tools



* [Practical Pangenome Graphs](https://pangenome.github.io/)

* [awesome-genome-visualization](https://cmdcolin.github.io/awesome-genome-visualization/) - specifically tools tagged with [Graph](https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Graph) and or [Pangenome](https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Pangenome)



# Contributions



Is something missing? Contributions are welcome, please make PRs to main or write an issue with a link.