• 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.

• Minigraph Fast method originally intended for 50+ bp SVs by Heng Li, produces rGFA format (not GFA or odgi)
• Cactus/minigraph Pangenome builder which aims to enable downstream compatibility. Produces GFA and odgi.
• PGGB Pangenome Graph Builder, calculates SNPs as part of the pipeline. Produces GFA and odgi.
• Pantools v3+ Fully featured construction of pangenome graphs
• PSVCP
• PHG Practical Haplotype Graph
• PATO R package for pangenome construction
• Chrom_mini_graph Generate and map reads onto a coloured minimizer pangenome graph

• vg map Original vg mapper (superseded by vg giraffe)
• vg giraffe Faster and more modern alternative to vg map
• 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

• vg call SNP caller for pangenomes, with gam or GAF output
• Paragraph
• Pangenie
• vg call surject to linear reference, then use linear SNP caller like Freebayes, Deepvariant etc
• Deepvariant Case study of deep variant SNP calling on vg giraffe aligned bam files

• vg call
• GraphTyper
• Pangenie

• Panagram
• Bandage Visualize GFA files
• SeqTubemap Elegant path visualization for smaller regions of a pangenome from the vg team
• VAG Visualization of short sequence alignments in a pangenome
• Panache View linearized pangenomes
• Waragraph
• PanGraphViewer
• Wally View GFA (Work in progress 2023)
• VRPG View rGFA or GFA, written in python and html
• Pantograph is a commercial option
• PGV A web based viewer similar to SeqTubeMap

• vg - generates static images
• odgi - generates static images

• vg validate
• odgi validate

• GFA An assembly interchange format read by both vg and odgi
• 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
• odgi Easy interconversion to main interchange format GFA.
• 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 Created by vg giraffe.

• 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

• PanKmer

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