Plasmid Assembly Use Of Cisa Contig Intergrator

Question

[bobo]

Hi everyone

Iv assembled a plasmid sequence and wanted to check whether I have done it correctly

1. I first obtained read mapped contigs
2. I secondly assembled contigs DE Novo using torrent assembler
3. I then inputted these contigs onto CISA contig integrator, this resulted in a single contiguose sequence
4. I then mapped my reads to the contiguose sequence and found an area of misaligned reads
5. I split my contiguouse sequence at this point and ended up with 2 contigs
6. I extended the two ends of the contigs by blasting my split contigs with my DeNovo contigs from another sequencing run I had
7. I have now a circular genome that seems to have good read mapping and coverage. The read mapping at the ends of the contig is good. Was my use of CISA contig integrator correct? Im worried that if I add contigs from two methods the contiguouse sequence may have two copies of fragments.

p.s. im using Iontorrant single end reads (400bp)

Note: my main goal was to sequence a chromosomal sequence, i found out that i had a plasmid sequence when i blasted my contigs that did not map well onto contiguator

[HG]

I also follow similar approch : but i use SeqMan for merging and got good result.