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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.

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    $\begingroup$ Welcome to the site! What is the depth of your sequencing? Did you assemble it already? Is there any reference genome of your organism? Also it would help to give a better answer if you showed what have you searched/tried. $\endgroup$ – llrs Apr 15 '19 at 7:23
  • $\begingroup$ Hi, thanks for your answer. The depth of my sequencing is 100×. The raw data is 2G, and has already assembled by sequencing company. There are two reference genome which i want to compare with, Bacillus amyloliquefaciens FZB42，Bacillus subtilis 168. $\endgroup$ – Ys Lu Apr 16 '19 at 5:33
  • $\begingroup$ Ok, this information is useful. Now the most important thing, what have you done to compare the annotations/annotate it yourself? You mention you had some problems finding resources, could you please provide the search terms you used, so we can avoid them and provide help about how to find the resources? $\endgroup$ – llrs Apr 16 '19 at 9:49
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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

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