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?
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.
You can map your data against your reference genome to see what it looks like
One clean option to obtain an annotated new genome would be to do de novo assembly (Mira, SPAdes,...) then do a draft genome from this. I like PAGIT.
This tool compile several softwares : abacas, image, icorn and ratt allowing you to do scaffold building, gap closing, iterative mapping and genome annotations. This may help
Sorry these tools are working with Linux.
I would recommend you to invest some time to acquire basics and install Linux, it will be a gain of time for most of the bioinformatic analysis you will undertake
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?