Support for .vg and other graphical genome data formats

[ekg]

I'd like to use vgraph to compare different "variation" graphs, in the vg sense.

Could vgraph or its algorithms be applied to the DAG-like parts of generic genome graphs?

[bioinformed]

Hi Erik,

vgraph is implemented to handle fairly linear diploid graphs, but could easily be extended to support arbitrary DAGs. The constraint propagation system was always intended to handle such cases. Additional work on path collapsing may also be needed to avoid exponential time searches, but that is a minor extension to the current model.

I'm certainly interested in adding such support. Can you point me in the direction of the best file formats and perhaps some simple example datasets?

Thanks, -Kevin

On Thu, Jun 28, 2018 at 5:39 AM, Erik Garrison [email protected] wrote:

I'd like to use vgraph to compare different "variation" graphs, in the vg https://github.com/vgteam/vg sense.

Could vgraph or its algorithms be applied to the DAG-like parts of generic genome graphs?

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