• Notes on the variant/variation graph
  • Introduction
  • WIP
  • GFA

Notes on the variant/variation graph

Introduction

In this repository I am recording an exploratory path through the variation graph (VG) also known as variant graph and pangenome. The goal is to come up with a new reference implementation that is (kinda) language agnostic, i.e., more of a documentation effort with implementation(s). The reference implementation aims to support:

1. Multiple in-memory graph storage solutions

2. Bindings for languages such as Python, Julia and Racket

3. Mix data from many sources (short reads, long reads, RNA-seq etc)

4. Support metadata and annotation

Based on this reference implementation we should be able to build out functionality as modular extension.

WIP

Checked out some sources in opensource/vg

Notes:

ODGI has a python module. Odgi node.cpp and node.hpp contain packing hacked_vector bit packed (hacked pack vector)

libbdsg has a slightly more obvious implementation of the packed graph

GFA

https://gfa-spec.github.io/GFA-spec/GFA2.html

GFA2 is overly complicated. Question is how far we need to support it.