Question: estimate genome coverage
0
gravatar for Ric
13 months ago by
Ric140
Australia
Ric140 wrote:

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

masurca kmergenie assembly • 667 views
ADD COMMENTlink modified 13 months ago by dbrowne.up60 • written 13 months ago by Ric140
1
gravatar for dbrowne.up
13 months ago by
dbrowne.up60
United States
dbrowne.up60 wrote:

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).

ADD COMMENTlink written 13 months ago by dbrowne.up60
0
gravatar for Medhat
13 months ago by
Medhat6.9k
Poland
Medhat6.9k wrote:

you can use bedtools like this calculate coverage


Or GATK

ADD COMMENTlink modified 13 months ago • written 13 months ago by Medhat6.9k
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