Variant Graph Support to BioD

[Njagi Mwaniki]

Hello I’m Njagi Mwaniki,

I am part of the 2019  Google Summer of Code under the Open 
Bioinformatics Foundation with a project aimed to add variation 
graph support to BioD under mentors George Githinji and Pjotr 
Prins.

What are variation graphs? Well it’s sequence graph that is used 
to represent variation in a genome. Let me explain.

A sequence graph also an alignment graph, breakpoint graph, or 
adjacency graph is a bidirected graph in which the vertices 
represent segments of DNA and the edges represent adjacency 
between segments in a genome. (from Wikipedia)

Sequence graphs have long been proposed as a replacement for 
reference genomes which are linear structures/sequences of bases.

A variation graph is a sequence graph together with a set of 
paths representing possible sequences from a population[1]. 
Despite these ideas being around for a long time we haven’t yet 
been able to use sequence graphs in real life bioinformatics 
applications such as sequence alignment or determining homology. 
This is what we hope to speed up.

VG is a set of tools that already implements variation graphs but 
which is a bit broad in its focus. In this project we are 
building upon the existing tools and knowledge from VG and 
looking for ways to improve its performance in terms of lookups 
and also its application with small genomes, specifically viruses 
and smaller mammals such as mice.


[1] Variation graph toolkit improves read mapping by representing 
genetic variation in the reference