Sequencing depth

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→ How to calculate the optimal sampling depth

Typical sequencing depths in metagenomic studies

Sequencing depth (Sampling depth or → library size) is the number of sequenced bases for a given sample.

Increase in sampling depth in recent years

Shotgun metagenomic sequencing - human gut

Average sample size of whole-genome sequencing (WGS) samples of human gut metagenomes deposited at the NCBI short read archive. Median run size of each study was chosen to avoid dominating the results by larger studies.

How deep is enough for metagenomic shotgun sequencing?

It's a balance between sampling depth and number of samples (for a given budget).

  • Increasing sampling depth

    • led to increased detection of bacterial species and strains at lower abundance level.

  • Higher number of samples

    • will increase the statistical power to proof that our experimental findings are correct.

See also:

→ Coverage depth of a genome

→ How to calculate the optimal sampling depth

Read more

Ni et al., 2013. Scientific Reports

How much metagenomic sequencing is enough to achieve a given goal?

Statistical sample sizes and power calculations