I have assembled a virus genome using Ray resulting in approximately 5000 contigs. Now I want to build a scaffold of those contigs to get the full genome (I am aware of the fact that there might be some gaps in the genome).
I found one tool called Medusa to do this. Unfortunately, this tool cannot take a file above 50 MB and my contig file is about 156 MB.
Are there any other tools that can perform reference based scaffolding?
It would be great if anyone knows about genome scaffolding packages in Bioconda.