I have paired-end reads of a lactococcal strain and its assembly.
I want to determine the origin of a specific contig of interest to known if its from a plasmid or a chromosomal origin.
I tried mapping the reads using bbmap, extension of contigs to study the termini, etc. but so far I haven't be able to determine with confidence the origin of the contig I'm studying.
Do you have any other recommendation on what I should try to do that?
Thank you in advance for your help!