Dear All,
I am really lost how to do genome assembly of a resequencing NGS data got from Illumina platform. Could you please suggest me tools, softwares and a workflow in order to do genome assembly and functional gene annotation?
Thanks in advance.
could you clarify your project : what organism are you working with? why resequencing? what exactly is your purpose?
The organism in this case is leishmania infantum and we have the reference genome as we know and the purpose is to assemble whole genome sequence and gene annotation.
But you already have a reference genome? Then why do assembly? Do you want to improve the reference?
oh I thought that without reference you would have some difficulties to assemble your sequences. So should I prefer de novo?
But why would you do assembly when you already have a reference genome? Don't you mean mapping/alignment?