How is genome coverage / depth is determined?

Question

[dnaproteinstudy]

I have the raw R1 and R2 files of a bacterial genome sequence that have been assembled into contigs using spades. How can I calculate the genome coverage / depth? Thanks.

Answer 1

[dnaproteinstudy]

There seems to be ~ 40000000 raw reads (including both R1 and R2) of 150 bp paired end sequencing and after spades assembly the size is ~2000000 nucleotides. So its 3000x coverage?

[liorglic]

Almost correct. The thing is, the assembly may be incomplete, meaning that the genome might be larger than 2 Mb. You should divide by the estimated genome size, if you know it. There are also ways to estimate it using a k-mer analysis (e.g. GenomeScope). However, it looks like your data is extremely deep, so the assembly size you got is probably close to the real genome size, so looks like you have an average sequencing depth of ~3000x.

[dnaproteinstudy]

Thank you so much. I am a newbie to this research, but I'll try if I can find it using GenomeScope in Galaxy.

[dnaproteinstudy]

@liorglic, sequencing depth of ~3000x is normal?

[liorglic]

As I wrote above, 3000x is extremely deep (you can get very good assemblies with 100-200x).

[dnaproteinstudy]

Thank you