Jabba: hybrid error correction for long sequencing reads using maximal exact matches

Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is that this mapping is constructed with a seed and extend methodology, using maximal exact matches as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of maximal exact matches in the context of third generation reads are presented

Sustaining a federation of future internet experimental facilities

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Valuing flexibility in the migration to flexible-grid networks

Increasing network demand is expected to put pressure on the available capacity in core networks. Flexible optical networking can now be installed to increase network capacity in light of future traffic demands. However, this technology is still in its infancy and might lack the full functionality that may appear within a few years. When replacing core network equipment, it is therefore important to make the right investment decision between upgrading toward flexible-grid or fixed-grid equipment. This paper researches various installation options using a techno-economic analysis, extended with real option insights, showing the impact of uncertainty and flexibility on the investment decision. By valuing the different options, a correct investment decision can be made

Jabba: hybrid error correction for long sequencing reads

Background: Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. Results: In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is the use of a pseudo alignment approach with a seed-and-extend methodology, using maximal exact matches (MEMs) as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of MEMs in the context of third generation reads are presented. Conclusion: Jabba produces highly reliable corrected reads: almost all corrected reads align to the reference, and these alignments have a very high identity. Many of the aligned reads are error-free. Additionally, Jabba corrects reads using a very low amount of CPU time. From this we conclude that pseudo alignment with MEMs is a fast and reliable method to map long highly erroneous sequences on a de Bruijn graph

Dynamic and stochastic routing for multimodal transportation systems

The authors present a case study of a multimodal routing system that takes into account both dynamic and stochastic travel time information. A multimodal network model is presented that makes it possible to model the travel time information of each transportation mode differently. This travel time information can either be static or dynamic, or either deterministic or stochastic. Next, a Dijkstra-based routing algorithm is presented that deals with this variety of travel time information in a uniform way. This research focuses on a practical implementation of the system, which means that a number of assumptions were made, like the modelling of the stochastic distributions, comparing these distributions, and so on. A tradeoff had to be made between the performance of the system and the accuracy of the results. Experiments have shown that the proposed system produces realistic routes in a short amount of time. It is demonstrated that routing dynamically indeed results in a travel time gain in comparison to routing statically. By making use of the additional stochastic travel time information even better (i.e. faster), more reliable routes can be calculated. Moreover, it is shown that routing in the multimodal network may have its advantages over routing in a unimodal network, especially during rush hours