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  • 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,

  • #2


    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
    Last edited by Guest; 12-08-2012, 10:03 AM.

    Comment


    • #3
      How can we know whether it is total number or paired number?
      Thanks,

      Comment

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