Coverage statistics for sequence census methods |
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Authors: | Steven N Evans Valerie Hower Lior Pachter |
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Institution: | (1) Department of Mathematics, University of California, Berkeley, California, USA;(2) Department of Statistics, University of California, Berkeley, California, USA;(3) Department of Molecular and Cell Biology, University of California, Berkeley, California, USA |
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Abstract: | Background We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic
Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how this can be used to detect regions with anomalous coverage. This
modeling perspective is especially germane to current high-throughput sequencing experiments, where both sample preparation
protocols and sequencing technology particulars can affect fragment length distributions. |
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