Hi,
An open question : How do you manage a large number of samples in term of storage ( fastq, bam, vcf, ... ), of directory structure, DB, ... ? When the number of samples becomes big, it can be though to manage this in a clear and efficent way. Multiple species, multiple people have access to the data, etc...
So for you, what is the best way to manage this?
see How Do You Manage Your Files & Directories For Your Projects ?