Phage Fasta?

[leannmlindsey]

Hello! Thank you for your previous help. I now have a set of prophages identified by Prophage_tracer that I want to further investigate and I want to better understand the output files. I was hoping to find the candidate phages fasta sequence listed somewhere in the output files. The only fasta file that I see in the output is the *.SR.reads.fasta, and from what I can see, I think this is simply the sequence of each of the split reads? Is that correct? So I must use the candidate phage output file locations to cut out the appropriate sequence from the contigs? Would that be the correct way to get the phage sequence?