Refernce allignment query in bowtie2

[sells78]

Hi all,

Apologies for what I'm sure are basic questions but if you have a reference sequence and a number of other genomes sequenced from the same species, one can align these in bowtie 2. The output is SAM file.

(1) Can you test the SAM file in the same way you would for the reference genome using something like assemblathon which takes fastq files?

(2) If wanting to identify structural variants between a reference genome and a number of other genomes - can this all be done with bowtie 2 or is bowtie 2 only for initial alignment.

Thanks kindly for any responses