Daley T, Smith AD.. Predicting the molecular complexity of sequencing libraries. Nat Methods 10: 325-327

Department of Mathematics, University of Southern California, Los Angeles, California, USA.
Nature Methods (Impact Factor: 32.07). 02/2013; 10(4). DOI: 10.1038/nmeth.2375
Source: PubMed


Predicting the molecular complexity of a genomic sequencing library has emerged as a critical but difficult problem in modern applications of genome sequencing. Available methods to determine either how deeply to sequence, or predict the benefits of additional sequencing, are almost completely lacking. We introduce an empirical Bayesian method to implicitly model any source of bias and accurately characterize the molecular complexity of a DNA sample or library in almost any sequencing application.

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Available from: Timothy Daley, Apr 09, 2014
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    • "Assessment of raw library sequencing metrics. A: Percent molecular complexity is defined as the number of unique reads divided by the number of total reads in a sample, multiplied by 100% [Daley and Smith, 2013] as a function of millions of reads sampled. B: Whole-exome regions targeted by each technology and the region in common between all technologies. "
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    • "In particular the estimator will diverge to positive or negative infinity depending on whether the largest observed coverage count is odd or even. We introduced rational function approximations to obtain globally stable estimates that still satisfy the nice local properties of the Good-Toulmin estimator (Daley and Smith, 2013). A rational function approximation to a power series is a ratio of polynomials that asymptotically approximates the power series up to a given degree, "
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    • "Figure 4 Library complexity curves quantify library complexity and the diminishing returns as sequencing progresses. Library complexity is an estimate of the number of distinct molecules in the library (Daley and Smith 2013). The convexly shaped complexity curve plots the number of distinct molecules observed against the number of sequenced reads. "
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