I have paired reads from sequencing bacterial genome with Illumina MiSeq. I assembled them into contigs and now I have 4022 contigs with N50=72749, length of the longest contig 229883, number of mapped contigs 41 and reference genome (1.8 Mb chromosome + 3 plasmids) coverage 91.35%. And I don't know what to do with 3981 unmapped contigs. Do they contain any useful information or they can be removed from the further analysis? And what about plasmids? How to separate plasmid DNA from a bacterial chromosome? And how can I improve this assembly by sequencing by Sanger?
Thank in advance for an answer!