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bioinformed / vgraph

vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph representation of genomic variants in to precisely compare complex variants that are refractory to comparison by conventional comparison methods.
Apache License 2.0
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Support for .vg and other graphical genome data formats #9

Open ekg opened 6 years ago

ekg commented 6 years ago

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 commented 6 years ago

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 notifications@github.com 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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