KrisKieft
commented
1 year ago PropagAtE should work on the MAG. Just be careful that if the prophage is on its own contig, rather than integrated into a contig of the host, then maybe it was incorrectly binned. Prophages from other genomes or lytic viruses can often be incorrectly binned in a MAG. If it was binned correctly, then likely its there because the coverage is similar to that of the host MAG (that's usually how binning algorithms work) and therefore I'd actually expect it to be dormant. Worth a look though.
For the coordinate file, please see the respective section in the README. "manual method: if prophages were identified by a different method, a manually generate prophage coordinates file can be used with PropagAtE."
Hi, I got some MAGs using the binning method. I have identified prophage in MAG, and want to analyze the activation prophage. First, the MAG includes some contigs other than the whole genome sequence (just one sequence). Is the PropagAtE still work? Second, I identified prophage by other software (start and stop location in MAG's contig have known), how do I prepare the -v and -f input files? Thanks!