Off topic:What R packages and other tools are designed for .gb whole genome files sequence processing: multiple alignment and SNP calling, generating reports?

Question

[fashiondesignrussian]

What R packages and Windows software or web tools are designed for the .gb whole genome files sequence processing: multiple alignment and SNP calling, generating reports?

I want to run experiments on WGS MDR tuberculosis data from databases and the local. Please advise best software suits and R packages, most robust for data processing and building nice reports with charts and tables. If you know good book chapters and articles, tell me.

I tried Lasergene, SeqSphere, JMP, need more tools. I am new to WGS data processing. I had experience only with microarrays.

Thank you