Tuesday 3 May 2016

How many reads to sequence a genome?

Last year I posted about the Lander-Waterman equation used to calculate the number of reads needed to sequence a sample. I explained that this general equation (C = LN/G) can be rearranged to allow you to compute the number of reads (N) to sequence a genome of known size (G) with specific coverage (C) and using reads of a specified length (L). Today I finally finished my Calculoid NGS reads calculator to make it easier to access..feel free to use and reuse as you see fit.

1 comment:

  1. Nice one,
    Have you thought about a calculator for targeted sequencing experiments
    (replace genome size with target capture region size and add a factor for off-target reads).
    E.g. assume 80% on-target fraction on a 1MB region with 500x Coverage and PE100:

    N = (Coverage * TargetSize) / (Readlength * Offtargetfraction)

    N = (500 * 1Mbp ) / (200 * 0.8)
    N = 3.125 M reads

    That's how we calculate our targeted experiments...


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