- 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- vg map Original vg mapper (superseded by vg giraffe)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
- 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
- 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
Is something missing? Contributions are welcome, please make PRs to main or write an issue with a link.