Table 2. Comparison of the Cost of Whole-Genome Sequencing and Exome Capture Based on Genome Size
SpeciesAnalysisSize of Target (Mb)Reads for 20× Coverage (Million)Capture CostTotal Costa
All speciesbExome capture4020.040307
Arabidopsis thalianaWGS13513.50180
SorghumWGS23023.00307
FlaxWGS35035.00467
RiceWGS38038.00507
Poplar, bananaWGS∼50050.00667
CassavaWGS75075.001,000
TomatoWGS90090.001,200
SoybeanWGS1,115111.501,487
MaizeWGS∼2,300230.003,067
TobaccoWGS∼3,000300.004,000
Tetraploid wheatWGS∼11,0001,100.0014,667
Hexaploid wheatWGS∼15,9601,596.0021,280
Northern SpruceWGS∼20,0002,000.0026,667
• a Sequencing cost is based on 20× coverage over the targeted space. For whole-genome sequencing (WGS), the amount of sequence data required is calculated directly from the genome size space. For exome capture, efficiency is expected to be lower since not all reads are expected to be on target. Based on the results presented in this article, we estimated that 20× coverage of a 40-Mb targeted space would require 20 million reads. The current cost of one 100 PE HiSeq lane is estimated at 2000 and generates ∼150 million aligned reads (thus ∼13.3/M reads). For exome capture, the cost per sample was based on the sequencing of 2000 individuals and amounts to ∼$40 per sample to account for the cost of the capture reagents (currently$72,000 for 96 reactions for the Nimblegen SeqEZ developer library, $330 for Hybridization and Washing reagents [96 reactions], and$500 of Cot-1-equivalent DNA and \$3000 of Adaptor Blockers).

• b Cost of exome capture in polyploid species is expected to be higher than in diploid species because higher sequence coverage is needed to be able to detect mutations in a polyploid background and because the targeted space can be larger if homoeologous sequences cannot be targeted simultaneously.