coverage required

[oliviera]

Dear all,

I try to get an idea of the base coverage required for the different sequencing applications.
I didn t find any review on this subject so if you know a nice paper or can complete the followings, your are more than welcome:

- whole genome resequencing: 40x genome size (Nature 464, 587-591)
- SNPs call: 31x genome size (Genome Res. 2010. 20: 273-280)
- de novo genome modelling: 100x ??
- de novo transcriptome modelling: 100x??
- transcript expression studies: ??


Oliviera

[malachig]

The relationship between library depth and transcript expression profiling is discussed at some length in the supplementary materials of Nature Methods. 2010 Oct;7(10):843-847 (ALEXA-Seq).

The Trans-ABySS manuscript provides an example of de novo transcriptome assembly that might be helpful.

[francois.sabot]

- whole genome resequencing: 40x genome size (Nature 464, 587-591)

This amount of 'x' depend also of the size of your reads: longer reads need less coverage for the same efficiency