Estimating Sequencing Coverage

Next-generation shotgun sequencing approaches require sequencing every base in a sample several times for two reasons: You need multiple observations per base to come to a reliable base call. Reads are not distributed evenly over an entire genome, simply because the reads will sample the genome in a random and independent manner. Therefore many bases will be covered by fewer reads than the average coverage, while other bases will be covered by more reads than average. You need to account for this in your planning. This application note provides information on how to calculate the coverage required for an experiment, and how to estimate the number of flow cells or lanes you need to use.