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Pangenome graphs (review article on graph-based pangenomic methods)
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I pulled SHIMMER Sketch Graphs out #80

Closed adamnovak closed 4 years ago

adamnovak commented 4 years ago

I pulled "SHIMMER Sketch Graphs" out of the table of visualization tools, because I couldn't find a citation or a link for it, and I couldn't work out what to put in the new/different columns I was adding to the table.

@cschin, apparently this is your tool and might be part of https://github.com/cschin/Peregrine perhaps? Can you provide a link/reference for the visualization aspect of the tool?

subwaystation commented 4 years ago

As far as I am aware of, the initial source is https://medium.com/@infoecho/constructing-a-graph-for-genome-comparison-swiftly-d47dcd7eae5d. Pointing to script https://gist.github.com/cschin/0584a5ffd57bcf9bf5a970c1a9c580d8 which shows how the visualizations are generated. But I am not sure how one would integrate this into the paper.

ekg commented 4 years ago

It's OK that we don't include this. I suspect it will become well-known as works are published using it. But at the moment it's even more fresh than some things which I felt it might be a stretch to add (minigraph and seqwish for instance).