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How do I calculate coverage? | Oxford Nanopore Technologies

How do I calculate coverage?

Coverage describes the average number of reads at each position in a genome. It is normally referred to in terms of ‘x’ coverage (number of times the genome is sequenced). It is a common way to describe the amount of sequencing data you need for various applications such as variant detection.

To estimate average coverage from your dataset, divide the amount of data you have collected by the size of the genome you are sequencing:

Coverage = total amount of data / genome size

For instance, if you are sequencing human genome (3.1 Gb) and you have collected 100 Gb of data, the estimated average coverage will be 32.3x:

100 Gb / 3.1 Gb = 32.3

To estimate how much data you will need to achieve your desired average coverage, multiply the size of the genome you are sequencing by the required coverage:

Total amount of data = genome size * coverage

For instance, if you are aiming to achieve 20x coverage of mouse genome (2.7 Gb), you will require at least 54 Gb of data:

2.7 Gb * 20 = 54 Gb

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