Hi,

We sequenced a plasmid on MiSeq, 150bp reads. I have a reference, and an expected sequence of the insert. I want to know at what position does the insert begin in the plasmid.

So far I have generated contigs using plasmid SPAdes, and bactopia. Neither align to the insert.

Some questions:

1. how can i turn these contigs into a whole genom for the plasmid?
2. Should I be using plasmid SPAdes if we didnt sequence the bacteria, only the plasmid?

Thanks,