Question: What Is The Sequencing 'Depth' ?
27
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum92k wrote:

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

thanks.

next-gen sequencing • 97k views
ADD COMMENTlink modified 7 months ago by jokipokemon00010 • written 7.1 years ago by Pierre Lindenbaum92k
20
gravatar for Casey Bergman
5.6 years ago by
Casey Bergman17k
Manchester, UK
Casey Bergman17k wrote:

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).

ADD COMMENTlink written 5.6 years ago by Casey Bergman17k

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

ADD REPLYlink written 5.4 years ago by Random150

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

ADD REPLYlink written 5.4 years ago by Casey Bergman17k
11
gravatar for Istvan Albert
7.1 years ago by
Istvan Albert ♦♦ 70k
University Park, USA
Istvan Albert ♦♦ 70k wrote:

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

ADD COMMENTlink written 7.1 years ago by Istvan Albert ♦♦ 70k
1

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

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

ADD REPLYlink written 22 months ago by paulorapazote40

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.

ADD REPLYlink written 22 months ago by Istvan Albert ♦♦ 70k
8
gravatar for Chris Miller
7.1 years ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

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.

ADD COMMENTlink written 7.1 years ago by Chris Miller18k
42
gravatar for Eric Normandeau
7.1 years ago by
Eric Normandeau9.2k
Quebec, Canada
Eric Normandeau9.2k wrote:

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!

ADD COMMENTlink modified 5.6 years ago • written 7.1 years ago by Eric Normandeau9.2k
1

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

ADD REPLYlink written 5.6 years ago by Bach540

@BaCh: Corrected

ADD REPLYlink written 5.6 years ago by Eric Normandeau9.2k

Does very high depth means that there is an artifact?

what should be the ideal depth of a true variant?

ADD REPLYlink written 19 months ago by jigarnt30
1
gravatar for Rks
7.0 years ago by
Rks20
European Union
Rks20 wrote:

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".

ADD COMMENTlink written 7.0 years ago by Rks20
0
gravatar for Madhan
5.6 years ago by
Madhan210
United States
Madhan210 wrote:

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.

ADD COMMENTlink written 5.6 years ago by Madhan210
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