FrAnTK: A Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets

Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyse their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualisation of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.

Efficient circuit design for content-addressable memory in quantum-dot cellular automata technology

Quantum-dot cellular automata (QCA) technology is a kind of nanotechnology utilized for building computational circuits. It can be a good technology for overcome CMOS drawbacks at nano-scale due to its low delay and area. The Content-Addressable Memory (CAM) is a very fast memory that can perform search operations in a very short time. This feature makes the relative popularity of these memories and many applications for them, especially in network routing and processors. In this study, a novel loop-based circuit is designed for the QCA memory unit, which reduces area, cell count, latency, and cost. The obtained results using QCADesigner tool version 2.0.3 demonstrate that the designed QCA memory unit utilizes 16 cells, 0.01 µm2 area, and 0.25 clock cycles and has a reduction of 33% in the number of cells, 50% in area, 50% in latency, and 75% in cost compared to existing works. Then, this memory unit is utilized to design an efficient structure for CAM circuit. The results show that the developed structure for CAM circuit has 0.75 clock cycles, 32 cells, and 0.03 µm2 area, and it has a reduction of 20% in the number of cells, 25% in area, 40% in latency, and 75% in cost compared to existing works.

CMOS Implementation of 5T SRAM with Low Power Dissipation

SRAM is a very fast memory with low power consumption. The main objective of this work is to perform a 64-digit SRAM with 90 nm innovation. Execution depended on a granular perspective. SRAM's base module is similar to an N-MOS inverter, flip-flop, and semiconductor. We design this module according to the configuration rule of the ? format. Using Harvard technology, SRAM can easily retrieve information from memory. To create advanced rational circuits, it is important to see how an SRAM is assembled and how it works. The bottom line is that with 0.12 micron 90nm technology, we are developing a 5T SRAM and we can read and write. It is a fundamental part of a computer's central processing unit. RAM is a building block made up of several circuits. The 64-bit SRAM reader was developed with MICROWIND and DSCH2. With the MICROWIND program, the developer can design and simulate an integrated circuit at the physical description level. DSCH2 allows switching of digital logic design.

UMGAP: the Unipept MetaGenomics Analysis Pipeline

Shotgun metagenomics is now commonplace to gain insights into communities from diverse environments, but fast, memory-friendly, and accurate tools are needed for deep taxonomic analysis of the metagenome data. To meet this need we developed UMGAP, a highly versatile open source command line tool implemented in Rust for taxonomic profiling of shotgun metagenomes. It differs from state-of-the-art tools in its use of protein code regions identified in short reads for robust taxonomic identifications, a broad-spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, a non-monolithic design, and support for interactive visualizations of complex biodiversities.

Time-Memory Analysis of Parallel Collision Search Algorithms

Parallel versions of collision search algorithms require a significant amount of memory to store a proportion of the points computed by the pseudo-random walks. Implementations available in the literature use a hash table to store these points and allow fast memory access. We provide theoretical evidence that memory is an important factor in determining the runtime of this method. We propose to replace the traditional hash table by a simple structure, inspired by radix trees, which saves space and provides fast look-up and insertion. In the case of many-collision search algorithms, our variant has a constant-factor improved runtime. We give benchmarks that show the linear parallel performance of the attack on elliptic curves discrete logarithms and improved running times for meet-in-the-middle applications.

GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes. As haploid chromosome-level assemblies are now commonly achieved for all types of organisms, phasing assemblies has become the new frontier for genome reconstruction. Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity. We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

Non-volatile optical switch of resistance in photoferroelectric tunnel junctions

In the quest for energy efficient and fast memory elements, optically controlled ferroelectric memories are promising candidates. Here, we show that, by taking advantage of the imprint electric field existing in the nanometric BaTiO3 films and their photovoltaic response at visible light, the polarization of suitably written domains can be reversed under illumination. We exploit this effect to trigger and measure the associate change of resistance in tunnel devices. We show that engineering the device structure by inserting an auxiliary dielectric layer, the electroresistance increases by a factor near 2 × 103%, and a robust electric and optic cycling of the device can be obtained mimicking the operation of a memory device under dual control of light and electric fields.