SVIM: Structural Variant Identification using Mapped Long Reads

Motivation: Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities. Results: We present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from PacBio and Nanopore sequencing machines. Availability and implementation: The source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index. Supplementary information: Supplementary data are available at Bioinformatics online

Quantum Flux and Reverse Engineering of Quantum Wavefunctions

An interpretation of the probability flux is given, based on a derivation of its eigenstates and relating them to coherent state projections on a quantum wavefunction. An extended definition of the flux operator is obtained using coherent states. We present a "processed Husimi" representation, which makes decisions using many Husimi projections at each location. The processed Husimi representation reverse engineers or deconstructs the wavefunction, yielding the underlying classical ray structure. Our approach makes possible interpreting the dynamics of systems where the probability flux is uniformly zero or strongly misleading. The new technique is demonstrated by the calculation of particle flow maps of the classical dynamics underlying a quantum wavefunction.Comment: Accepted to EP

Space probe/satellite ejection apparatus for spacecraft

An ejection apparatus for spinning and propelling objects for ejection from a spacecraft at a desired velocity and rotational speed is discussed. The apparatus includes a launch cradle on which the space object to be ejected rests. The cradle is rotatably supported by a central hub secured to the upper end of the pneumatic cylinder piston shaft. Release mechanisms consisting of a retractable pin and locking lug is utilized to hold the cradle and object to be ejected. The release mechanism has a fixed barrier member which holds the retractable pin in engagement with the locking lug until release by upward movement of the launch cradle beyond the barrier height

Scarring by homoclinic and heteroclinic orbits

In addition to the well known scarring effect of periodic orbits, we show here that homoclinic and heteroclinic orbits, which are cornerstones in the theory of classical chaos, also scar eigenfunctions of classically chaotic systems when associated closed circuits in phase space are properly quantized, thus introducing strong quantum correlations. The corresponding quantization rules are also established. This opens the door for developing computationally tractable methods to calculate eigenstates of chaotic systems.Comment: 5 pages, 4 figure

Multiple Scattering Theory for Two-dimensional Electron Gases in the Presence of Spin-Orbit Coupling

In order to model the phase-coherent scattering of electrons in two-dimensional electron gases in the presence of Rashba spin-orbit coupling, a general partial-wave expansion is developed for scattering from a cylindrically symmetric potential. The theory is applied to possible electron flow imaging experiments using a moveable scanning probe microscope tip. In such experiments, it is demonstrated theoretically that the Rashba spin-orbit coupling can give rise to spin interference effects, even for unpolarized electrons at nonzero temperature and no magnetic field.Comment: 34 pages, 7 figure

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

Motivation With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes. Results We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual. Availability and implementation SVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/svim-asm

Modelling the quark propagator

The quark propagator is at the core of lattice hadron spectrum calculations as well as studies in other nonperturbative schemes. We investigate the quark propagator with an improved staggered action (Asqtad) and an improved gluon action, which provides good quality data down to small quark masses. This is used to construct ans\"{a}tze suitable for model hadron calculations as well as adding to our intuitive understanding of QCD.Comment: Lattice2002(spectrum

Observing trajectories with weak measurements in quantum systems in the semiclassical regime

We propose a scheme allowing to observe the evolution of a quantum system in the semiclassical regime along the paths generated by the propagator. The scheme relies on performing consecutive weak measurements of the position. We show how weak trajectories" can be extracted from the pointers of a series of measurement devices having weakly interacted with the system. The properties of these "weak trajectories" are investigated and illustrated in the case of a time-dependent model system.Comment: v2: Several minor corrections were made. Added Appendix (that will appear as Suppl. Material). To be published in Phys Rev Let

Experience with a "social model" of capacity building: the Peoples-uni

<p>Abstract</p> <p>Background</p> <p>Taking advantage of societal trends involving the "third sector", a social model of philanthropy and the open-source software and educational resource movements, provides the opportunity for online education for capacity building at low cost. The Peoples Open Access Education Initiative, Peoples-uni, aims to help build public health capacity in this way, and this paper describes its evolution.</p> <p>Methods</p> <p>The development of the Peoples-uni has involved the creation of an administrative infrastructure, calls for and identification of volunteers, development of both the information and communications technology infrastructure and course content, and identification of students and course delivery to them. A pilot course module was offered for delivery.</p> <p>Results and Discussion</p> <p>Volunteers have been prepared to become involved in the administrative structures, as trustees, members of advisory and quality assurance and educational oversight groups. More than 100 people have offered to be involved as course developers or as facilitators for course delivery, and to date 46 of these, from 13 countries, have been actively involved. Volunteer experts in information and communications technology have extended open-source course-delivery mechanisms. Following an encouraging pilot course module, 117 students from 23 countries have enrolled in the first set of six course modules. Although the business model is not fully developed, this approach allows current module delivery at USD 50 each, to be more affordable to the target audience than traditional university-based education.</p> <p>Conclusion</p> <p>A social model of capacity building in public health has been started and has been able to attract volunteers and students from a wide range of countries. The costs are likely to be low enough to allow this method to make a substantial contribution to capacity building in low-income settings.</p