I have a problem related to characterizing a novel plasmid genome of a coccus species bacteria.
I have Illumina 2X150 sequenced reads of plasmid. The data was assembled in scaffolds. Now I realize that there can be contamination of genomic scaffolds, so I blastN the scaffolds to NT and separated the scaffolds with plasmid hits and genomic hits. Now my question is:
What are the minimum features to say that certain scaffolds belong to the plasmid concerned or I have covered the entire plasmid in scaffolds at all ? and what are the ways to build a circular map ? (I got this tool called SnapGene but i guess i have to sequentially arrange the scaffolds isn't ?)