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

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

Miniature photonic-crystal hydrophone optimized for ocean acoustics

This work reports on an optical hydrophone that is insensitive to hydrostatic pressure, yet capable of measuring acoustic pressures as low as the background noise in the ocean in a frequency range of 1 Hz to 100 kHz. The miniature hydrophone consists of a Fabry-Perot interferometer made of a photonic-crystal reflector interrogated with a single-mode fiber, and is compatible with existing fiber-optic technologies. Three sensors with different acoustic power ranges placed within a sub-wavelength sized hydrophone head allow a high dynamic range in the excess of 160 dB with a low harmonic distortion of better than -30 dB. A method for suppressing cross coupling between sensors in the same hydrophone head is also proposed. A prototype was fabricated, assembled, and tested. The sensitivity was measured from 100 Hz to 100 kHz, demonstrating a minimum detectable pressure down to 12 {\mu}Pa (1-Hz noise bandwidth), a flatband wider than 10 kHz, and very low distortion

Team trust and team learning in new product development teams

Farklı örgütsel seviyelerde güven ve öğrenme üzerine yapılan çalışmaların yanı sıra, güvenin takım bağlamında bilgi paylaşımı ve edinimi için önemli bir faktör olduğunu bildiren birtakım çalışmalar bulunmaktadır. Ancak bugüne kadar yeni ürün geliştirme takımlarında (new product development – NPD) Takım Güveni ve Takım Öğrenmesi ilişkileri hakkında çok az tartışma yapılmıştır. Bu çalışma, Takım Güveninin, çeşitli takım faktörleri (Takım Üyesi Deneyimi, Takım İstikrarı ve Takım Otonomisi) ve Takım Öğrenimi arasında arabuluculuk etkisi olup olmadığını incelemeyi amaçlamaktadır.Besides studies on trust and learning at different organizational levels, there are a number of studies reporting that trust is an important factor for knowledge sharing and acquisition in team context. So far, however, there has been little discussion about Team Trust and Team Learning relations in NPD teams. This study focuses on examining whether there is a mediational effect of Team Trust between various team level factors and Team Learning