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graph-genome / graph-genome.github.io

Graph Genome Documentation
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graphgenome.org is down #30

Open SingingMeerkat opened 2 years ago

SingingMeerkat commented 2 years ago

Hello to the pantograph team!

I tried to access the pantograph version made during the biohackathon in 2020, but the whole website is unavailable and most of the hyperlinks within this GitHub project does not work for me anymore. Has it been taken down? and hopefully archived somewhere? Is it related to the newest version of pantograph that is being developed?

Thanks for your time and attention!

subwaystation commented 2 years ago

Hi there @SingingMeerkat,

unfortunately, the project was not further developed since the biohackathon 2020.

@josiahseaman is working in the industry.

I was focusing on the pre-processsing steps for the visualization of a pangenome graph. For example using a Path-Guided Stochastic Gradient Descent - PG-SGD algorithm to linearize a graph in 1D. For example see https://odgi.readthedocs.io/en/latest/rst/tutorials/sort_layout.html.

@joehagmann brought some back-end parts from Python to C++: https://github.com/joehagmann/odgi/tree/pantograph_output. However, Computomics' front-end implementation itself is not open-source. You can find a demo at https://pantograph.computomics.com/. Using it will cost something. I don't know the details, though.

Maybe we should flag this project and repository as discontinued? What do you think?

As alternatives, I would take a look at https://github.com/chfi/gfaestus or the recently updated https://github.com/asl/BandageNG/tree/v0.9.6. Maybe you want to extend your https://github.com/SouthGreenPlatform/panache? The most similar tool compared to Pantograph is https://github.com/chfi/waragraph I think.

Hope I could help.

Best, Simon

SingingMeerkat commented 2 years ago

Hi @subwaystation and others,

Many thanks for all these details! I have only followed from afar after the biohackathon and was not (fully) aware of how the project evolved.

A disclaimer warning about the project's discontinuation would be a good idea, I think. I wanted to reference it as it was still working not too long ago; I hoped that there would be an archived version somewhere, at least for a "proof of concept" of sort.

Panache will not be updated soon, I first need to finish working on my PhD dissertation and another project. There will be future additions but nothing properly planned yet! I was really interested in pantograph's visual representation of pangenomes and wanted to mention it among other examples of possible pangenome visual representations. waragraph was unkown to me until today, I will take a look, thanks!

It did help, thanks again Simon!

Best, Eloi

subwaystation commented 2 years ago

Hi @SingingMeerkat

you are welcome. I added a warning on the top of the README.