estimate genome coverage

Question

[Ric]

Hi, I ran KmerGenie and I got the best Kmer and the estimated genome size. How do I get the estimated genome coverage?

Thank you in advance.

Best wishes,

Mic

Answer 1

[dbrowne.up]

Or more broadly and easily... C = R x L / G

Where C is physical coverage, R is the total number of reads, L is (average) read length, and G is the genome size.

So for example, if you have a 100 Mbp genome and an Illumina library with 10 M reads of length 150 bp, the coverage of the genome is 15X (10,000,000 * 150 bp / 100,000,000 bp).

Answer 2

[Medhat]

you can use bedtools like this calculate coverage

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Or GATK