I have a circular plasmid sample which was sequenced on MiSeq PE 300. I performed a de novo aseembly using
SPAdes. The contig which I obtained is 11526 bp long. The reference sequence for this plasmid is 12089bp long. When I BLAST the reference sequence against the de novo assembled contig I get the BLAST with Plus/Minus stand orientation as follows:
I did reverse complement of the reference and performed alignment again but it is aligning in the same orientation. I loaded the assembly in sequencher. I had to split the assembly into two fragments this introduced a long gap in the alignment as below from 10480 bp to 10999 bp. Sequencher output:
- How can I get a complete assembly of the genome from the PE 300 reads of a circular plasmid?
- Is there a way to renumber the bases in the de novo assembled sequence so that it aligns correctly without introducing a gap.