Calculate sampling depth

Calculate how deep sequencing for a required genome coverage.

genomeLength x coverage x 100 / abundance = samplingDepth

genomeLength - bacterial genome length

coverage - required coverage

abundance - expected relative abundance level (percent)

Example

Genome length: 5Mbp

Required coverage: 2X

expected abundance level: 0.5 %

5Mbp x 2 x 100 / 0.5 = 2Gbp

5,000,000 x 2 x 100 / 0.5 = 2,000,000,000

A sampling size of 2Gbp is required to get a 2X coverage of a 5Mbp genome present at 0.5% abundance level

How many reads? (for example: 200bp read length)

samplingDepth / readLength

2,000,000,000 bp / 200 bp = 10,000,000 reads