As far as I understood, for most assembly programs, the scaffolding step takes into consideration paired-end information in order to get from contigs (contiguous sequences) to scaffolds (longer sequences that might have some N-filled gaps).
My assembly software of choice, MEGAHIT, uses paired-end information to build the contigs, but it does not output a standard scaffold. So I am wondering the following, related things:
-is it meaningful to run a scaffold program on the output of MEGAHIT? I imagine there might be some instances in which paired-end information could span a gap.
-Which software would you recommend for it? (I've tried soapdenovo2 and SSPACE, but they appear not to be actively maintained so I have the issue of 'it doesn't work and I can't do anything about it')
-Could relevant information (eg. two contigs being connected by pair-end information) be recovered by alternative and perhaps more user-friendly means, such as exploring the assembly graph with Bandage?
Thank you for your time!