What Is The Sequencing 'Depth' ?

Question

[Pierre Lindenbaum]

I often see the word depth in the manuals of the tools for NGS, what is its meaning ?

thanks.

Answer 1

[Casey Bergman]

Eric gives the correct answer for depth (of coverage). I think confusion in this area stems not from the term "depth" but from the term "coverage". Coverage now appears to have 3 meanings:

1. the theoretical "fold-coverage" of a shotgun sequencing experiment: number of reads * read length / target size
2. the theoretical or empirical "breadth-of-coverage" of an assembly: assembly size / target size
3. the empirical average "depth-of-coverage" of an assembly: number of reads * read length / assembly size

(1) and (3) are not the same because of sequencing error & unclonable/unmappable regions of the genome. Lander-Waterman theory deals with the relationship between (1) and (2).

[Random]

Good clarification of the terms. Can you point me to paper references where these were first defined? Particularly depth and breadth of coverage. Or is this knowledge just "common sense"? Thanks

[Casey Bergman]

These are my attempt to make these concepts explicit. I am not aware of where they are stated together in one place.

Answer 2

[Istvan Albert]

I believe it is the same concept as coverage, it might come from a shorthand of saying depth of coverage.

[paulorapazote]

http://www.nature.com/nrg/journal/v15/n2/full/nrg3642.html

Sequencing depth and coverage: key considerations in genomic analyses - Nature Reviews (2014)

[Istvan Albert]

A great review! Thanks for posting this link, I was not aware of its existance. Goes to show how seemingly simple concepts have many dimensions and complexities.

Answer 3

[Chris Miller]

It's also worth noting that you can use read depth to infer copy number, given a sufficient number of reads. On average, you'll get 1.5x more reads from a triploid region than you will from the rest of the diploid genome.

Answer 4

[Eric Normandeau]

Sequencing depth represents the (often average) number of nucleotides contributing to a portion of an assembly.

On a genome basis, it means that, on average, each base has been sequenced a certain number of times (10X, 20X...).

For a specific nucleotide, it represents the number of sequences that added information about that nucleotide.

Such depth varies quite a lot depending on the genomic region. In consequence, an average sequencing depth of 30X leaves a lot of small portions of a genome unsequenced while other receive a lot more sequences.

Cheers!

[Bach]

Small correction: the term does not apply only to "NGS" assemblies, but to all assemblies.

[Eric Normandeau]

@BaCh: Corrected

[jigarnt]

Does very high depth means that there is an artifact?

what should be the ideal depth of a true variant?

Answer 5

[Madhan]

I think, the depth means the coverage of the Sequencing technology only,

Coverage = (total number of bases generated) / (size of genome sequenced).

So a 30x coverage means, on an average each base has been read by 30 sequences. And the distribution in not always uniform. Some of the sequences may be covered more and some may be very less, so usually the coverage means an average value.

Answer 6

[Rks]

I believe that Depth refers to coverage itself which again means how many times a particular base is sequenced by NGS technology. I read this in the paper "A bioinformatian's guide to metagenomics".

Answer 7

[Renesh]

https://reneshbedre.github.io/blog/seqcov.html