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Welcome to the vg wiki!

In a hurry? Check our Quickstart guide or some Basic Operations.

Variation graphs are powerful objects capable of describing populations of genomes. vg provides a set of tools to construct, manipulate, and visualize them in the context of genome informatics.

Please feel free to edit and extend this wiki! For any questions or concerns please use the issues page in this repository, or drop by the vg chat on gitter or irc (#vg in freenode).

Tutorials

• Creating a graph from two E. coli assemblies: Graph & annotations for two E. coli strains
• Large genomes, from graph construction to read alignment: Working with a whole genome variation graph
• Simulate reads from a graph: Simulating reads with vg sim
• Linear vs. pangenome alignment comparisons: Evaluating alignment performance using simulation
• Aligning long RNA-seq reads to a GBZ-format pangenome: Long‐read RNA‐seq with pre‐existing pangenome

Basic usage

1. Get graph: Construction examples (or download a graph such as from the HPRC).
   WARNING! Note that nodes must be no more than 1024bp long. vg construct -m 1024 or vg mod -X 1024 will chop nodes down to size. Or construct with vg autoindex to do it automatically.
2. Simplify graph for better read alignment: Haplotype Sampling
3. Index graph:
   • automatically (vg autoindex): Automatic index construction
   • manually: Manual index construction
   • special considerations for large data: Dealing with huge datasets
4. Align reads:
   • short DNA-seq: Mapping short reads with Giraffe
   • short RNA-seq: Multipath alignments and vg mpmap (also see Transcriptomic analyses)
   • long: Mapping long reads with Giraffe
5. Call variants: SV genotyping and variant calling

Things you might need

• Export human-readable alignment information: Getting alignment statistics with vg filter
• Import and export linear references: Linear references and vg
• Modify which paths are considered "references": Changing references (also see Path Metadata Model)
• Visualize graphs: Introduction to visualization & Complex graph visualization
• Turn a graph into a VCF: VCF export with vg deconstruct
• Filter primers based on the pangenome: Primer Filter

General reference

• vg manpage
• Troubleshooting
• Giraffe best practices
• Building and manipulating GBWTs with vg gbwt
• Our internal Protobuf data model
• RDF
• File formats
  • master table: File Types
  • detailed descriptions: Extra details on vg file formats
  • GAF format (human-readable graph alignments): Graph Alignment Format in vg (or full GAF specification)
  • GAMP format (multipath graph alignments): Multipath alignments and the GAMP format

Understanding our data formats

• How we conceptualize graphs: Variation graphs
• How we break down graphs: Snarls and chains
• How we store paths: Path Metadata Model

VG Development

• Releases
• Roadmap
• Draft Changelog
• Testable Documentation
• Debian Packaging
• Programming with the vg API (extend our code yourselves!)