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).

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

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

• 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

• vg giraffe: Mapping short reads with Giraffe
• vg giraffe: Mapping long 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

• Visualization
• SV genotyping and variant calling
• Long read assemblies using vg msga
• Simulating reads with vg sim
• Transcriptomic analyses and RNASeq
• Long‐read RNA‐seq with pre‐existing pangenome
• Changing references
• Extracting a FASTA from a Graph
• VCF export with vg deconstruct
• Getting alignment statistics with vg filter

• Releases
• Roadmap
• Draft Changelog
• Testable Documentation

• 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

• Variation graphs
• Snarls and chains