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- vg Full featured construction, mapping and SNP calling toolkit based on multiple formats. 🚀
- odgi Fast toolkit based on odgi format 🚀
- gfatools Toolkit for GFA parsing and conversion
- gfakluge Toolkit and c++ API for GFA manipulation
- gaftools Toolkit for GAF (Graph Alignment Format) sorting and manipulation.
- gretl Statistics and analysis for GFA files, written in Rust
- pgr-tk A PanGenomic Research Took Kit, the unfortunate thing is that the output of this process is not a GFA file.
- Minigraph Fast method by Heng Li, produces referenceGFA (rGFA) format (not GFA or odgi) 🚀
- Cactus/minigraph 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
- 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- vg map Original vg mapper (superseded by vg giraffe)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
- 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
- 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
- pangenome. A comprehensive nf-core Nextflow pipeline using PGGB and odgi components. Better parallelized than PGGB alone. 🚀
- pangepop A snakemake pipeline to create a pangenome with minigraph-cactus and align reads against it with vg giraffe
- 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.
- 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.
Is something missing? Contributions are welcome, please make PRs to main or write an issue with a link.