Hello, I have Paired-end NGS reads from a fungi. Inspecting 16S RNA points that the genome may be Aspergillus japonicus or related to it.
My question is how can I assemble sequence reads so that I would nearly end up with assemblies approximating to different chromosomes?
I was able to use SOAPDenovo2 to assemble reads into contigs. But, that does not reveal anything about the number of chromosomes. This is my very first whole genome project and I am have no idea how to achieve this.
Can I further assemble contigs to get at least scaffolds? If I can, could you suggest me a tool.