Browsing by Subject "Assembly algorithm"

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    Dynamic threshold-based assembly algorithms for optical burst switching networks subject to burst rate constraints
    (Springer, 2010-04-17) Toksöz, M. A.; Akar, N.
    Control plane load stems from burst control packets which need to be transmitted end-to-end over the control channel and furtherprocessed at core nodes of an optical burst switching (OBS) network for reserving resources in advance for an upcoming burst. Burst assembly algorithms are generally designed without taking into consideration the control plane load they lead to. In this study, we propose traffic-adaptive burst assembly algorithms that attempt to minimize the average burst assembly delay subject to burst rate constraints and hence limit the control plane load. The algorithms we propose are simple to implement and we show using synthetic and real traffic traces that they perform substantially better than the usual timer-based schemes.
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    Improving genome assemblies using multi-platform sequence data
    (Springer, 2015-09) Kavak, P.; Ergüner, B.; Üstek, D.; Yüksel, B.; Saǧıroǧlu, M. Ş.; Güngör, T.; Alkan, Can
    Accurate de novo assembly using short reads generated by next generation sequencing technologies is still an open problem. Although there are several assembly algorithms developed for data generated with different sequencing technologies, and some that can make use of hybrid data, the assemblies are still far from being perfect. There is still a need for computational approaches to improve draft assemblies. Here we propose a new method to correct assembly mistakes when there are multiple types of data generated using different sequencing technologies that have different strengths and biases. We exploit the assembly of highly accurate short reads to correct the contigs obtained from less accurate long reads. We apply our method to Illumina, 454, and Ion Torrent data, and also compare our results with existing hybrid assemblers, Celera and Masurca. © Springer International Publishing Switzerland 2016.