Variant Graph Support to BioD

[Njagi Mwaniki]

On Tuesday, 28 May 2019 at 21:24:54 UTC, James Blachly wrote:
> On 5/28/19 5:41 AM, Njagi Mwaniki wrote:
>> 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.
>> ...
>> 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.
>
> This sounds like a great project.  Be aware that the size of 
> the organism (e.g. mouse) has naught to do with the size of its 
> genome.

Thank you.
With regards to the complexity of the genome, we're starting with 
a very small virus dataset and building up from it
https://github.com/urbanslug/GSoC-experiments/tree/master/data/RSV/refererence_and_vcf_file

The mouse is a possible application area of the genome really and 
a good place to test the robustness of the tool.