Currently I have 1 contig that contains 2 gaps, both gaps are approximately ~1,906bp collectively. This single contig is a collection of my data being run through multiple assemblers and stitched by hand. This is a chloroplast genome and I am trying to find a way to close these gaps and finalize my assembly. I have a significant amount of paired-end Miseq data (~300bp) and some PacBio data, although the PacBio data is less reliable due to shallow sequencing and errors.
Do you have any programs you would recommend? Techniques, protocols, papers? This project is my masters thesis and I would like to start running some analyzes on the complete chloroplast genome once I close these 2 gaps.
So far I have tried blasting my data to the surrounding regions of the gaps to try and extend the bp/sequence into the gaps, using sort of a "crawl-assembly" method but it hasn't worked. I also tried blasting the PacBio data onto the single contig (since PacBio data are huge pieces of sequence) but that hasn't worked.
Any suggestions would be greatly appreciated!