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pangenome / smoothxg

linearize and simplify variation graphs using blocked partial order alignment
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Generate consensus from smoothed graph #177

Closed BaxW closed 1 year ago

BaxW commented 1 year ago

I have graphs I've made with pggb, but I want to make consensus graphs from them. As I understand, building a consensus graph is still disabled within pggb. With that in mind, how can I run smoothxg on the graphs I get from pggb to produce a consensus myself? It seems like

smoothxg -g pggb_graph.gfa -o consensus_graph.gfa -C cons,100 -n -H <file>

Is close to what I would want in order to generate the consensus without prepping or smoothing again, but I don't understand what file to pass to -H. I know it should contain consensus path names, but where would these names come from if I haven't made a consensus yet? Would this be the same file that would be output with smoothxg -f ?

Thanks!!!

BaxW commented 1 year ago

Closing because it is now possible to add -C to pggb call and generate consensus.