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.
