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VG Balanced Bundle Decomposition

Algorithms to find balanced bundles and use them to further decompose a variation graph.

Project Objectives

Ongoing Objectives

  • Integrate with vg's snarl manager to reduce "irreducible" subgraphs.

Theory

Reduction Rules

Rule 1

alt text

Rule 2

alt text

Rule 3

alt text

Tools

  1. Graph Assistant (Python3)
    Create and convert custom test graphs. Supports custom vg-inspired JSON format, vg compliant JSON format, and old legacy JSON format.

Contributors

Current

  • Christopher Liu (Undergraduate Researcher) [GitHub]
  • Yohei Rosen M.D. (Ph.D. Candidate)

Former

  • Ryan Nishimoto (Undergraduate Researcher) [GitHub]

Works Referenced

  1. (2017) Describing the Local Structure of Sequence Graphs - Yohei Rosen, Jordan Eizenga, and Benedict Paten [link]