I have a bacterial genome assembly that contains contamination from plasmid vector sequences. How can I remove the contaminants from the assembly file?"
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.
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy