Converting to a single connected component

[JoshuaDanielRubin]

Hello,

I was wondering, is it possible to ensure that PGGB will produce a graph that has only a single connected component? Alternatively, which parameters can I pass to make it more likely that the resulting graph will have a single connected component?

[AndreaGuarracino]

You can try reducing -s, -l, and -p parameters in order to get more mappings that would keep everything in a single connected component. However, be aware that the alignment will become much slower, and also the next steps.

[subwaystation]

This also assumes that all input sequences can somehow! be aligned to each other in a way that they will form only one single connected component!