Shallow Sequencing Vs Deep Sequencing

Question

[Joe]

Hi,rookie question.

What is the difference between deep sequencing and shallow sequencing? Is it just the difference of coverage?

When do you apply deep/shallow sequencing?

Answer 1

[Neilfws]

An interesting observation regarding the term "deep sequencing": if you search the Web or PubMed for that phrase, a clear and concise definition is not readily apparent.

It's an ugly and unhelpful term because it implies (incorrectly) that there are basically 2 types of sequencing: deep and shallow, without defining what is meant by either of them.

Yes, it is basically about coverage. But how much coverage counts as "deep"? 10x ? 25x ? 500x ? When we were using Sanger sequencing to sequence genomes, 10x might have been called "deep". Now with so called "next generation" technologies (another unhelpful term), anything from tens to hundreds might be called "deep".

My advice: the most important thing is that you understand the principles behind each kind of sequencing technology. Avoid the jargon and the meaningless buzz phrases; they are not helpful.

Answer 2

[Ying W]

I believe shallow/deep usually refer to coverage. 30x coverage (for humans) is used as standard coverage. When sequence coverage is much higher than that it is 'deep sequencing' while 'shallow sequencing' would refer to lower coverage. When you pay for something to be sequenced, you pay for the # of lanes and you know each lane will give you about a certain number of base pairs so depending on how many lanes of sample you run you have a general idea what the coverage will be.

These terms are also \used for different sequencing technologies. Short read sequencers (ex. illumina) you can get high coverage easily while it is much harder to get high coverage from long read sequencing technologies (ex pac bio).

Answer 3

[maduh17]

To determine copy number variation, it is enough to do "shallow" whole genome sequencing, at 0.1-0.2X coverage.

To confidently call mutation in heterogenous population of cells, for example in cancer, you might want to go for "deeper" coverage, at 80X or higher.

For relatively homogenous cells such as your blood, people go for 40 to 50X.