Insert sequence in plasmid (plasmidid)

Question

[aLex97]

I have WGS data that includes the genome and plasmid with a gene of interest. How can I identify the insert within the plasmid using bioinformatics tools? I've tried using PlasmidID, but I'm not sure how to interpret the results.

Thank you in advance!

Answer 1

[Pierre Lindenbaum]

map your wgs data on https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/ , remove any read mapping on a plasmid, BLAST vs 'nr' the remaining reads ?