What is your biological question?
First and foremost you should ask yourself what is it that you are trying to answer with high throughput sequencing data. A hypothesis driven experiment will always be more insightful and easier to design than an experiment without direction.
Common feedback given by grant review panelists that feel a researcher is sequencing samples without a clear direction or hypothesis.
There are four main aspects that should be considered to answer your biological question during experimental design: biological system, sequencing technology and cost.
The organism or group of organisms that a researcher or group of researchers are studying.
Multiple copies of the same genome contained in a single nucleus due to a recent whole genome duplication event
An organism that has had a whole genome duplication in the ancient past (millions of years) but has rediploidized
- Repeat Content
The amount of highly repetitive sequences contained in the genome.
- GC Content
The percent GC or AT in your genome can affect the quality of the sequencing data that you acquire. Some sequencing technologies and assembly programs have trouble with AT rich genomes.