How to distinguish plasmids and chromosome when I analyze data from next generation sequencing?

Question

[silvia.caprari84]

Hi all,

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)?

Thanks

[GenoMax]

While not foolproof plasmid DNA can be expected to show a much deeper coverage (since there will be multiple copies). There is a plasmid specific version of popular assembler SPAdes (plasmid SPAdes) that you could try. If you have not assembled this data as yet then SPAdes would be a good place to start.

Answer 1

[BioinfGuru]

Surely comparison of the sequence with that of a recent non-resistant ancestor will tell you if the resistance gene is on a plasmid.