I have two similar genomes (one "known", one "unknown"). The "known" genome has already been determined to contain a plasmid. Both Prokka and plasmidspades have unexpectedly shown no results for plasmids in either genomes. In the case of plasmidspades, I ran the following commands:
plasmidspades.py - 9,21,33,55,77,127 --careful -1 read1.fastq -2 read2.fastq plasmidspades.py - 9,21,33,55,77,127 -1 read1.fastq -2 read2.fastq
In both cases, there was no contigs.fasta in the main output directory, the assembly_graph.fastg in the main output directory was empty, the warnings.log in the main output directory said "No putative plasmid contigs found!", and inside the directories (such as K127), the final_contigs.fasta was empty. Unless I should check elsewhere in the Prokka outputs, I interpret this to mean no plasmids were found.
So, I then downloaded the plasmid sequence fasta file on GenBank (that had already been discovered for the "known" genome). Using BWA, I aligned the raw reads from the genomes to this plasmid reference fasta file. In the "unknown" genome, I see 180 reads mapping to the plasmid reference fasta file. I believe this is evidence that the "unknown" genome contains a plasmid (even if undetected by Prokka and plasmidspades).
*My question is - *
What approach should I take to solidify the evidence for the presence/absence of plasmid(s) in this "unknown" genome? If there is a plasmid present, how can I determine its sequence with confidence? (Side note: For the "unknown" genome, I have the raw reads, the assembled contigs from running SPAdes, and the reordered contigs from running MAUVE against the "known" genome as a reference).