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

Scalable Multifunctional Ultra-thin Graphite Sponge: Free-standing, Superporous, Superhydrophobic, Oleophilic Architecture with Ferromagnetic Properties for Environmental Cleaning.

Water decontamination and oil/water separation are principal motives in the surge to develop novel means for sustainability. In this prospect, supplying clean water for the ecosystems is as important as the recovery of the oil spills since the supplies are scarce. Inspired to design an engineering material which not only serves this purpose, but can also be altered for other applications to preserve natural resources, a facile template-free process is suggested to fabricate a superporous, superhydrophobic ultra-thin graphite sponge. Moreover, the process is designed to be inexpensive and scalable. The fabricated sponge can be used to clean up different types of oil, organic solvents, toxic and corrosive contaminants. This versatile microstructure can retain its functionality even when pulverized. The sponge is applicable for targeted sorption and collection due to its ferromagnetic properties. We hope that such a cost-effective process can be embraced and implemented widely

The effects of post-deposition annealing conditions on structure and created defects in Zn0.90Co0.10O thin films deposited on Si(100) substrate

We analyze the effect of post-deposition annealing conditions on both the structure and the created defects in Zn0.90Co0.10O thin films deposited on the Si (100) substrates by RF magnetron sputtering technique using home-made targets. We concentrated on understanding the homogeneity of substituted Co+2 ions and the annealing effects on the amount of defects in the ZnO lattice. Orientations of thin films are found to be in the [0002] direction with a surface roughness changing from 67±2 nm to 25.8±0.6 nm by annealing. The Co+2 ion substitutions, changing from 7.5±0.3 % to 8.8±0.3 %, cause to form Zn–O–Co bonds instead of Zn–O–Zn and split the Co2p energy level to Co2p1/2 and Co2p3/2 with 15.67±0.06 eV energy difference. In addition, the defects in the lattice were revealed from the correlations between Zn–O–Co bonds and intensity of Raman peak at around 691 cm-1. Furthermore, the asymmetry changes of O1s peak positions in X-ray Photoelectron Spectra (XPS) were also found to be in accordance with the Raman results

High level rule modeling language for airline crew pairing

The crew pairing problem is an airline optimization problem where a set of least costly pairings (consecutive flights to be flown by a single crew) that covers every flight in a given flight network is sought. A pairing is defined by using a very complex set of feasibility rules imposed by international and national regulatory agencies, and also by the airline itself. The cost of a pairing is also defined by using complicated rules. When an optimization engine generates a sequence of flights from a given flight network, it has to check all these feasibility rules to ensure whether the sequence forms a valid pairing. Likewise, the engine needs to calculate the cost of the pairing by using certain rules. However, the rules used for checking the feasibility and calculating the costs are usually not static. Furthermore, the airline companies carry out what-if-type analyses through testing several alternate scenarios in each planning period. Therefore, embedding the implementation of feasibility checking and cost calculation rules into the source code of the optimization engine is not a practical approach. In this work, a high level language called ARUS is introduced for describing the feasibility and cost calculation rules. A compiler for ARUS is also implemented in this work to generate a dynamic link library to be used by crew pairing optimization engines