Finding Insert in plasmid

Question

[SaltedPork]

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,

[GenoMax]

Neither align to the insert.

Does this mean you can't find the expected insert when you try to align?

See Identification of the sequence insertion site in the genome for inspiration.

You could also use bbduk.sh in filter mode to see if you are able to find reads that align to the expected insert. Guide for bbduk.sh here: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/