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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