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Welcome to the vg wiki!

In a hurry? Check our Quickstart guide.

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).

First things first

• Building VG (or not building vg)
• Building VG on Cent OS 6.6 or 7 and using it

VG's formats and some basic usage

• File Formats
• Basic Operations
• Haplotype Sampling
• Considerations for Batch Processing
• Programming with the vg API
• Path Metadata Model

Graph / index construction

• Graph construction from a reference and a VCF file
• Index types
• Automatic index construction
• Manual index construction
• Building and manipulating GBWTs with vg gbwt
• Dealing with huge datasets

Read alignment

• vg giraffe: Mapping short reads with Giraffe
• vg giraffe: Giraffe best practices
• vg giraffe: Mapping to a personalized reference with Haplotype Sampling
• vg mpmap: Multipath alignments and vg mpmap
• vg map: Working with a whole genome variation graph

Other VG tools

• Visualization
• SV genotyping and variant calling
• Long read assemblies using vg msga
• Simulating reads with vg sim
• Transcriptomic analyses
• Changing references
• Extracting a FASTA from a Graph
• VCF export with vg deconstruct

VG Project Management

• Releases
• Roadmap
• Draft Changelog
• Testable Documentation

VG RDF

• RDF:-for-VG
• Example:-Serving-out-an-RDF-version-of-a-VG-graph-with-Apache-Fuseki
• Example: Serving out an RDF version of a VG graph with Blazegraph
• Annotating-a-VG-graph-the-RDF-way
• 2 ecoli genomes, with ensembl and uniprot annotation