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Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most(More)
Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate(More)
MOTIVATION With advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found(More)
This paper proposes a novel approach to check the authenticity of hardware based on the inevitable performance gap between real hardware and simulations or emulations that impersonate it. More specifically, we demonstrate that each processor design can be authenticated by requiring a checksum incorporating internals of complex micro-architectural mechanisms(More)
Suppose we sample n haplotypes, observing their alleles at each of two loci and obtaining configuration n = (a, b, c). Here c = (c ij) is a matrix of the counts of haplotypes for which both alleles were observed; c ij is the number of haplotypes with allele i at the first locus and allele j at the second locus. We also allow for the possibility that a(More)
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