Calculating sequence coverage

tahamasoodi · 12-08-2012, 09:33 AM

How can we calculate the coverage of Illumina paired end whole genome sequencing data using Waterman equation? Example data is given:

Total reads = 450,000,000
Read length = 101
Genome size = 3000000000

12-08-2012, 09:53 AM

http://www.illumina.com/Documents/pr...alculation.pdf

The Lander/Waterman equation is a method for computing coverage.
The general equation is:

C = LN / G

• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads

So, if we take one lane of single read human sequence with v3 chemistry, we get

C = (100 bp)*(189×10^6)/(3×10^9 bp) = 6.3

This tells us that each base in the genome will be sequenced between six and seven times on average.

---------------------

Though take care whether the "total reads" number is really the number of all reads (read 1 + read 2) or actually the "total pair" number. In the first case, you can just do the equation, however if it's the latter then you need to

C = 2*LN/G

tahamasoodi · 12-08-2012, 10:28 AM

How can we know whether it is total number or paired number?

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12-08-2012, 09:33 AM	#1
tahamasoodi Success Location: India Join Date: May 2012 Posts: 130	Calculating sequence coverage How can we calculate the coverage of Illumina paired end whole genome sequencing data using Waterman equation? Example data is given: Total reads = 450,000,000 Read length = 101 Genome size = 3000000000 __________________ Thanks,

12-08-2012, 09:53 AM	#2
lorendarith Guest Posts: n/a	http://www.illumina.com/Documents/pr...alculation.pdf The Lander/Waterman equation is a method for computing coverage. The general equation is: C = LN / G • C stands for coverage • G is the haploid genome length • L is the read length • N is the number of reads So, if we take one lane of single read human sequence with v3 chemistry, we get C = (100 bp)(189×10^6)/(3×10^9 bp) = 6.3 This tells us that each base in the genome will be sequenced between six and seven times on average. --------------------- Though take care whether the "total reads" number is really the number of all reads (read 1 + read 2) or actually the "total pair" number. In the first case, you can just do the equation, however if it's the latter then you need to C = 2LN/G Last edited by lorendarith; 12-08-2012 at 10:03 AM.

12-08-2012, 10:28 AM	#3
tahamasoodi Success Location: India Join Date: May 2012 Posts: 130	How can we know whether it is total number or paired number? __________________ Thanks,