Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201

Investigation of Parameters Affecting Underwater Communication Channel

Underwater communication has become a widely studied area in recent years and showed great potential to be an area of research. Acoustic communication is often preferred in underwater communication due to its suitability for an underwater diffusion environment. However, in underwater communication, the physical and chemical properties of the water environment affect sound propagation. Therefore, determining and examining parameters affecting channel performance in underwater communication plays an essential role in inefficient communication. In this study, the effects of salinity, depth, noise, temperature, and frequency parameters for the underwater channel model are examined. By determining the effects of these parameters on spherical and cylindrical propagation, suitable propagation geometry and parameter values for an efficient channel are investigated. In light of the results obtained, in case of studying in a limited area, the path and absorption losses can be reduced by selecting cylindrical propagation as a geometrical propagation model, thereby an efficient channel model can be formed

Transition of free convection flow inside an inclined parallel walled channel: effects of inclination angle and width of the channel

Transition of free convection flow in an inclined parallel walled channel has been investigated numerically by employing k–ɛ turbulent model. Particular attention is paid on how the inclination angle and width of the channel affect the transition process of the flow developing in the channel. The upper plate of the channel is heated isothermally and facing downward, while the lower one is kept under the adiabatic condition. The inclination angle of the channel is varied from 0° to 85° with respect to its vertical position while the distance separating the two plates is systematically reduced from 0.45 to 0.06 m. Distributions of velocity, turbulent kinetic energy and local heat flux are presented to examine the critical distance and the results obtained show good agreement with experimental data available in the literature

Permutation Trellis Coded Multi-level FSK Signaling to Mitigate Primary User Interference in Cognitive Radio Networks

We employ Permutation Trellis Code (PTC) based multi-level Frequency Shift Keying signaling to mitigate the impact of Primary Users (PUs) on the performance of Secondary Users (SUs) in Cognitive Radio Networks (CRNs). The PUs are assumed to be dynamic in that they appear intermittently and stay active for an unknown duration. Our approach is based on the use of PTC combined with multi-level FSK modulation so that an SU can improve its data rate by increasing its transmission bandwidth while operating at low power and not creating destructive interference for PUs. We evaluate system performance by obtaining an approximation for the actual Bit Error Rate (BER) using properties of the Viterbi decoder and carry out a thorough performance analysis in terms of BER and throughput. The results show that the proposed coded system achieves i) robustness by ensuring that SUs have stable throughput in the presence of heavy PU interference and ii) improved resiliency of SU links to interference in the presence of multiple dynamic PUs.Comment: 30 pages, 12 figure