What tool is best to build plasmid using a reference sequence?

Question

[blur]

Hi,

I have a plasmid assembled using both short and long reads.

Also, I have other WGS samples, sequenced before using illumina short reads that contain the same plasmid

I want to use the assembled plasmid as a reference/scaffold to build upon.

Can anyone direct me to the right tool? Is there such an option in Unicycler?

Also - is the right path using an aligner like BWA or bowtie2?

[Pierre Lindenbaum]

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[blur]

After reading some more - should I map to reference with an aligner like BWA? or is there an assembly tool that uses a reference?