Telescoper: de novo assembly of highly repetitive regions.

MotivationWith advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.ResultsIn this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.AvailabilityTelescoper is publicly available for download at sourceforge.net/p/[email protected] informationSupplementary data are available at Bioinformatics online

Swarm shape manipulation through connection control

The control of a large swarm of distributed agents is a well known challenge within the study of unmanned autonomous systems. However, it also presents many new opportunities. The advantages of operating a swarm through distributed means has been assessed in the literature for efficiency from both operational and economical aspects; practically as the number of agents increases, distributed control is favoured over centralised control, as it can reduce agent computational costs and increase robustness on the swarm. Distributed architectures, however, can present the drawback of requiring knowledge of the whole swarm state, therefore limiting the scalability of the swarm. In this paper a strategy is presented to address the challenges of distributed architectures, changing the way in which the swarm shape is controlled and providing a step towards verifiable swarm behaviour, achieving new configurations, while saving communication and computation resources. Instead of applying change at agent level (e.g. modify its guidance law), the sensing of the agents is addressed to a portion of agents, differentially driving their behaviour. This strategy is applied for swarms controlled by artificial potential functions which would ordinarily require global knowledge and all-to-all interactions. Limiting the agents' knowledge is proposed for the first time in this work as a methodology rather than obstacle to obtain desired swarm behaviour

High-ordered spectral characterization of unicyclic graphs

In this paper we will apply the tensor and its traces to investigate the spectral characterization of unicyclic graphs. Let $G$ be a graph and $G^m$ be the $m$-th power (hypergraph) of $G$. The spectrum of $G$ is referring to its adjacency matrix, and the spectrum of $G^m$ is referring to its adjacency tensor. The graph $G$ is called determined by high-ordered spectra (DHS for short) if, whenever $H$ is a graph such that $H^m$ is cospectral with $G^m$ for all $m$, then $H$ is isomorphic to $G$. In this paper we first give formulas for the traces of the power of unicyclic graphs, and then provide some high-ordered cospectral invariants of unicyclic graphs. We prove that a class of unicyclic graphs with cospectral mates is DHS, and give two examples of infinitely many pairs of cospectral unicyclic graphs but with different high-ordered spectra