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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.
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