Our team recently sequenced a whole genome (WG) of bacterial isolate and performed denovo assembly of that bacterial isolate. Currently I am planning to do following things
1) Compare the WG sequenced bacterial isolate to other publicly available sequences of Escherichia or any other deposited sequences in NCBI. I am thinking of doing BLAST against the custom database. Creating the custom database of all Escherichia isolates and blasting it against my WG sequenced bacterial isolate. Am I correct with my approach?
2) I received another similar strain of WG sequenced bacterial isolate from our collaborator. I would like to compare our team's WG sequenced isolate (isolate A) with our collaborator's isolate B and identify SNPs between the two isolates. I have used GATK for SNP identification for human samples. But for bacterial sequences what methods/tools are used?
I am open for any other recommendations to the above requirement 1 and 2. Any suggestions.