I am currently trying to perform a new assembly using paired and mate paired reads. I first mapped my paired-end on a reference genome. Now I would like to extract from the mapping only the covered portions and get contigs from my reads (not a consensus with the reference genome including N between the uncovered portions). I would like then to use the paired-end reads and the mate paired to scaffold my assembly.
I there a proper way to do that ? I think maybe mpileup could help, but until now I only managed to produced consensus.
Extra question, which software would you recommend to perform the scaffolding ? Does any one exist allowing different insert size ?
Thank you very much !!!