Genome annotation of a Bacillus strain I finished the sequencing of the genome of a biocontrol activity strain Bacillus amyloliquefaciens by Illumina hiseq. I have already gone through some papers but there were no details of processing in it.  

Is anywhere I can find some resources to get my research going on to genome annotation, compare it with other microbial genome data, and analyze non-ribosomal peptide synthetase, find out more genomic information about biocontrol activity?

For example, how to locate 16S DNA and some lipopeptide antibiotic genes (fungycin gene, surfactin gene) in my bacterial genome, and compare it with the reference strain and draw a phylogenetic tree. And how to use my bacterial genome and 2 reference genomes to draw a genomic circle diagram.
You said that you want to compare with other microbial genome data. Have you already annotated your genome? If not, you might consider a pipeline I've developed, I can gladly help if you face some problems using it.

It is called bacannot, it does a complete annotation using Prokka, Kofam, CARD, VFDB, and other resources. It might help you to have a first scratch of your data since it also collapses annotation information in a genome browser