I understand that with Pacbio error rate (~15%), it is not really suitable for SNP calling.
This is maybe a naive question, but I was wondering if we have, for example, a really high coverage sequencing of a bacteria (>200X), wouldn't it make it possible to call SNP anyway?
If so, what would be the most cleaver way to do that? Try to do the "classic" way, align to a reference genome and detect variants (is there any tool doing that?). Or maybe perform a genome assembly, and then align the assembly to the reference ?
Has anyone tried that already?
Thanks in advance for your inputs