Hi,

Sequencing coverage means, how much of your targeted genomic region is covered. Suppose your targeted region is 50MB and your platform has sequenced 45MB of your interest. So your coverage is 90%. Now come the point of depth. In simple words, depth of a genomic postion is equal to number of reads aligned to that positon.

As Sir Daniel said, it is still a challenge for molecular biologists to design probes for complete genomic region. That actually leads to the urge for checking coverage and depth of sequencing. As per my knowledge, the researchers used to say 20X coverage, that means targeted region is covered with an average read depth of 20 (correct me if I am wrong).

There are lots of way to calculate depth and covearge. I have my own scripts to calculate these aspects. SAM file can be paresed for the same purpose. Also some stand alone tools those can serve you the purpose.

Hope these will help.

Good luck

The distinction isn't clear. As a matter of fact, most folks would use "depth" as shorthand for "depth of coverage." This simply reflect the average number of times a given region has been sequenced by independent reads.

In many cases, a given NGS dataset won't encompass the entirety of a target genome, because certain regions are difficult to sequence and/or map (repetitive DNA, or sequences that align to multiple places in the genome). Therefore, even if your depth of coverage is good in most regions, depth of coverage is not constant across a genome and some regions may effectively have no coverage. In addition, some people will assess coverage in terms of assembled genome size vs. target genome size, essentially "breadth of coverage." Don't confuse this with depth of coverage (# reads * read length / size of target genome). HTH.

Hi,

Sequencing coverage means, how much of your targeted genomic region is covered. Suppose your targeted region is 50MB and your platform has sequenced 45MB of your interest. So your coverage is 90%. Now come the point of depth. In simple words, depth of a genomic postion is equal to number of reads aligned to that positon.

As Sir Daniel said, it is still a challenge for molecular biologists to design probes for complete genomic region. That actually leads to the urge for checking coverage and depth of sequencing. As per my knowledge, the researchers used to say 20X coverage, that means targeted region is covered with an average read depth of 20 (correct me if I am wrong).

There are lots of way to calculate depth and covearge. I have my own scripts to calculate these aspects. SAM file can be paresed for the same purpose. Also some stand alone tools those can serve you the purpose.

Hope these will help.

Good luck

Hey,

The terms coverage and depth can be a bit confusing and different people will use them to mean different things.

I will go with Sourav and say that in my opinion coverage refers to the percentage of genome covered while depth refers to the number of reads per genome base. Note here that there is a variation of the depth of coverage which is reads / genome base covered. I haven't seen this one used much, but it is a valid alternative.

As to tools, i have a nice and quick implementation of computing both coverage and depth here: https://github.com/CosteaPaul/qaTools.

Many thanks to Daniel, Sourav and Paul. I also got some information from the Biostar website (http://www.biostars.org/p/638/):

(1) Sequencing coverage:

Currently, coverage appears to have 3 meanings:

(a) the theoretical "fold-coverage" of a shotgun sequencing experiment: number of reads * read length / target size

(b) the theoretical or empirical "breadth-of-coverage" of an assembly: assembly size / target size

(c) the empirical average "depth-of-coverage" of an assembly: number of reads * read length / assembly size

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

(2) Sequencing depth:

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.

can you provide some examples?

Very informative answers above. Thank you

This helped alot. Thanks

Helpful. Thank you

Finding these answers/comments useful too. Moving into molecular things and so need to update myself

Very useful discussion. Also, please find further details here: http://www.nature.com/nrg/journal/v15/n2/full/nrg3642.html

They are used as alternative. Coverage means how many times your target sequence been sequenced in order to make sure that your variant has been detected with high degree of confidence

Mohamed Hussain coverage doesn't mean that, It shows sequenced length (how much portion of the complete sequence covered). Depth shows ..' how many times your target sequence been sequenced in order to make sure that your variant has been detected with high degree of confidence '.

Naveen Chaudhary, excellent descriptions, very ilustrative, thank.