How do I calculate the number of reads to have 500X coverage after the Target enrichment?

First of all, you need to know the size of the Enrichment panel. For example, the size of the Panel is 240 kb and you used 2 X 75 bp read length (75 x 75 cycles). We also assume that you had 90% Duplication rate. So, the 500X coverage is only calculated for the de-duplicated reads. Here is how you can calculate:
1. Panel size – 240 kb
2. Multiply the Panel size by 5000X (reads before deduplication) – 240kb x 5000 = 1.2 x 10^9 bases
3. Divide this number by the number of sequencing reads (75+75=150 bases) – 1.2x 10^9 / 150 = 8,000,000 paired reads (or 16 million total)
4. We assume that the Hybridization Capture efficiency is about 30%. So, should add 30% more reads – 8 x 10^6 reads +4x 10^6 = 12 million reads per samples (or 24 million total reads).