Hi! The sample I am using for analysis is plasmid DNA. I performed assembly of the reads using SPAdes and plasmid identification using Recycler. However the plasmid being identified is 1000 bases in size whereas the original construct is 5000 bases in size. What can be the reason for it?

Also, how useful is homology based approach in this. Say, I filter all the contigs above 5000 bases and above in size and BLAST them.

Thanks in advance!