From linear strings to graphs

Question

[mcgalpeter]

As new researcher and having started my PhD studies less than one year, I had a conversation with a Bioinformatician at a conference this summer in Dublin who explain that one of the next big steps is moving from linear strings to graphs and I found it interesting.

Do you agree? Are there related papers? I would like to listen opinions from experts.

Answer 1

[Pierre Lindenbaum]

A few links:

• http://www.genomebiology.com/2015/16/1/13
• http://genomicsandhealth.org/files/public/GA4GH%20Meeting%20June%20Beacon%20Project%20and%20Data%20Sharing%20APIs.mp4 at 13'
• https://docs.google.com/presentation/d/1utWF1_Er6bfAAwYWWRvDL-XI73uFC17WNi45t-TXveM/edit?usp=sharing

Answer 2

[WilliamS]

See also this MIT technology review article: http://www.technologyreview.com/news/537916/rebooting-the-human-genome/

This picture below I think also gives a good overview of the idea of a string graph reference genome. Aligning reads or whole genomes to this graph would lead to a path, or a new path (?) trough this string graph reference genome.

It will take time before a this works and even more time before it will be implemented and usable. But a very cool, useful and necessary development.

There will be a meeting on string graph reference genomes by GA4GH members on October 13th at the New York Genome Center.

http://ga4gh.org/#/oct2015meeting

Some papers (which I got from here https://github.com/ga4gh/schemas/wiki/Human-Genome-Variation-Map-(HGVM)-Pilot-Project):

Paten, Novak, Haussler paper describing approaches to constructing a reference structure

Novak, Rosen, Haussler, Paten paper describing mapping to a reference structure (only deals with string to string case, but concept generalises)

Dilthey, Cox, Iqbal, Nelson, McVean paper describing applications of a graph-based reference structure to inference in the MHC