How to remove cloning vector sequence from bacterial assembled genome?

Question

[mathavanbioinfo]

Hi All I have a bacterial genome assembly that contains contamination from plasmid vector sequences. How can I remove the contaminants from the assembly file?"

[GenoMax]

You could use an alignment program and vector reference to identify the vector (if it was assembled as a single piece in your data).

Ideally you need to start over. Clean the reads of vector contamination first followed by redoing the assembly.