Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

Abstract

Multiple re-sequencing approaches have been developed and reviewed (McCormack et al. 2013a ; Lemmon and Lemmon 2013). Below, we briefl y summarize the major re-sequencing methods, indicating their advantages and disadvantages (Table 3.1) and the scale at which they are most appropriate (Fig. 3.1). For all methods, we assume that sequencing coverage will be reasonably deep to achieve high accuracy (Table 3.2), especially at heterozygous sites. All methods are usually paired with DNA sequence tags (also known as barcodes, indexes, or molecular identifi ers, MID tags; see Faircloth and Glenn 2012) to identify individual samples from a pool of samples. We assume that lower costs will increase how widely the techniques will be adopted, and that total costs of ≤$100 US/sample, including personnel costs, are highly desirable.