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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1101/2023.04.05.535718
MIT License
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what dose "consensus path" generated with parameter -Q mean #378

Open yipukangda opened 4 months ago

yipukangda commented 4 months ago

Hi,

pggb has a parameter -Q to give consensus path a prefix name in the smoothxg step, what dose "consensus path" mean and where could I find it(I searched in gfa file but get no results).

thanks

AndreaGuarracino commented 4 months ago

smoothxg can add (into the final graph) consensus sequences obtained by performing partial order alignment in each graph block during graph normalization. However, such a feature is currently disabled in pggb. I should probably hide the -Q parameter for a while!

yipukangda commented 4 months ago

Thanks, if I use smoothxg independently with this function, dose it mean this step could merge all similar sequence within a block into one?