Contigs Input For Phylogenetic Tree

Question

[davidmaimoun]

Hello,

I want to create a nextstrain phylogenetic tree from multifastas (on bacteria strains).

The problem is my assemblies are contigs.

Is concatenate the contigs is a good (and easier) way to get the complete sequence, or I need scaffolding (and if scaffolding needed, what tool do you advise)?

Thank you very much