I need to analyse results coming from next generation sequencing on bacterial 3 strains that are carbapenem-resistant. I am using the software "Artemis" to analyze the sequences. I anticipate that this stuff is totally new for me. I am particularly interested in the resistance genes and in the determination of their genetic environment. I was wondering how I can understand from the sequencing data if the resistance genes are on plasmids or on the chromosome?How can I distinguish plasmids and chromosome by the sequencing data?What kind of problems or issues can I encounter when I analyze the data?Is there anything to which I should be more careful in the analysis of the data (e.g. could the sequencing method create contigs that don't correspond to the real aspect of the genome)?