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What Is The Sequencing 'Depth' ?

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

thanks.

next-gen sequencing
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

7 answers

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).

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updated by Ram Ram • written by Casey Bergman Casey Bergman

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

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written by Random Random

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

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written by Casey Bergman Casey Bergman

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

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updated by Ram Ram • written by Istvan Albert 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.

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written by Istvan Albert Istvan Albert

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.

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written by Chris Miller Chris Miller

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!

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written by Eric Normandeau Eric Normandeau

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

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written by Bach • Bach

Does very high depth means that there is an artifact?

what should be the ideal depth of a true variant?

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written by jigarnt • jigarnt

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.

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written by Madhan • Madhan

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".

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written by Rks • Rks

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

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written by Renesh Renesh

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