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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
• Considerations for Batch Processing
• Programming with the vg API
• Path Metadata Model

VG Project Management

• Releases
• Roadmap
• Draft Changelog
• Testable Documentation

VG tools in detail

• Visualization
• Working with a whole genome variation graph
• Automatic index construction
• Manual index construction
  • Index types
  • Building and manipulating GBWTs with vg gbwt
  • Dealing with huge datasets
• Construction
• Alignment
• Mapping short reads with Giraffe
• Whole-genome calling and genotyping
• Long read assemblies using vg msga
• SV genotyping with vg
• Simulating reads with vg sim
• Multipath alignments and vg mpmap
• Transcriptomic analyses
• Changing references
• Extracting a FASTA from a Graph

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