plasmidspades copy number

Question

[greenhorn]

hi, is it possible to predict copy number of plasmids using plasmidSpades? have run it on paired end genome seqs, opened the contigs in geneious software and assembled. how can i use the output data best in geneious and how can i annotate? it does only annotate the restriction sites when using plasmapper thanks a lot a total beginner

[Joe]

To my knowledge, not really.

You will see increased coverage if the plasmid is high copy number vs low copy number for instance, but that's about it. In principle I think it's possible to do, but you'd need multiple runs and some quite good standards I think, and you would basically be able to build up a kind of standard curve of coverage vs copy number. The problem here is that no 2 sequencing runs are ever really the same, so you might get more or less coverage each run, without it actually corresponding to a change in plasmid number.

To annotate, run something like prokka by Torsten Seeman.