Towards IMplicit Pangenome Graph Construction Tools

[subwaystation]

Description of feature

@ekg implemented https://github.com/ekg/impg, which allows to directly subset a given set of all-vs-all alignments into consecutive pieces. Using this approach and https://github.com/pangenome/gfalace, we would replace the RAM and disk space intensive SEQWISH with parallel runs of the PGGB workflow for each such piece. Later, we can lace these pieces together with gfalace.

I already did some first trials, but with questionable input: https://hackmd.io/@subwaystation/HJgaosEa6. I now know more and can get more into the details.

Working on this issue would give us an idea on how to connect impg, gfalace, and potentially other tools in order to add these to the pipeline.