I have to work with a genome assembly which consists of about 32000 scaffolds (obviously, the scaffolds are not annotated) as a reference for SNP calling. However, before proceeding further, I would like to:
1. Read about the process of making a genome assembly.
2. Get basic statistics of my genome assembly.
I have been searching to find a good review but I thought to ask if there is any particular review that you find it useful.
It would also be great if you could mention the basic statistics that one should calculate to know about the quality and properties of an assembly. I have this list, is there any other thing that should be added to it:
Coverage - Assembly Size - Total Contig Length - Scaffolds - Scaffold N50 - Contigs - Contig N50 - %Q40
Thank you in advance, Homa