data analysis of miseq pipeline on detecting multiple resistance

[[email protected]]

I would like built a pipeline for detect multiple resistance mechanisms from a big data base.
I got the raw sequencing data and would like run assembly,
my questions is that:
shall I do de novo assembly methods (Velvet) or using map too as BWA or blast?

[GenoMax]

You need to provide some more details to get actionable recommendations.

What big database are you referring to? What kind of sequencing have you done? Is this single isolates, pooled strain(s) or metagenomic data?