I have an Illumina PE data (2X 2,3GB, reads of 150bp) and I am trying to assemble a mitochondrial genome of ~500 Kb expected size. I used ABySS for contig generation and SSPACE for scaffolding. Finally, I got 65 scaffolds and i used MAUVE to order them against a reference genome.
My question is : How to concatenate scaffolds in order to obtain the complete genome sequence? Do I need to look for overlapping between them or just to merge scaffolds into a single fasta file ?
I tried CAP3 and BLAST for overlapping, but i did't find any overlaps.
Thank you in advance!