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

On the efficient computation of recurrence relations

A new parallel algorithm for the solution of a general linear recurrence is described. Its relation to the work of Kogge and Stone is discussed

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

Synthesis of atactic and stereoregular vinylaromatic polymers and a study of their reactions with alkali metals Final report

Synthesis and characteristics of atactic and stereoregular vinylaromatic polymers and their reactions with alkali metal

The Arbitrary Trajectory Quantization Method

The arbitrary trajectory quantization method (ATQM) is a time dependent approach to quasiclassical quantization based on the approximate dual relationship that exists between the quantum energy spectra and classical periodic orbits. It has recently been shown however, that, for polygonal billiards, the periodicity criterion must be relaxed to include closed almost-periodic (CAP) orbit families in this relationship. In light of this result, we reinvestigate the ATQM and show that at finite energies, a smoothened quasiclassical kernel corresponds to the modified formula that includes CAP families while the delta function kernel corresponding to the periodic orbit formula is recovered at high energies. Several clarifications are also provided.Comment: revtex, ps figure

Spectral analysis of 636 white dwarf - M star binaries from the Sloan Digital Sky Survey

We present a catalog of 857 white dwarf (WD)-M binaries from the sixth data release (DR6) of the Sloan Digital Sky Survey (SDSS), most of which were previously identified. For 636 of them, we complete a spectral analysis and derive the basic parameters of their stellar constituents and their distances from Earth. We attempt to measure fundamental parameters of these systems by completing spectral analyses. We use a Chi^2 minimization technique to decompose each combined spectrum and derive independent parameter estimates for its components. Forty-one of the stellar duets in our spectroscopic sample are optically resolved in their respective SDSS images. For these systems, we also derive a minimum true spatial separation and a lower limit to their orbital periods, typically which are some 10^4 yr. Spectra of 167 stellar duets show significant hydrogen emission and in most cases no additional He i or He ii features. We also find that 20 of the 636 WDs are fitted to be DOs, with 16 measured to have T_eff around 40,000 K. Furthermore, we identify 70 very low-mass objects, which are secondaries of masses smaller than about 0.1 solar masses, to be candidate substellar companions. Although various selection effects may play a role, the fraction 6.4 % of WD-M star binaries with orbital separations of around 500 AU is a criterion for evolutionary models of stellar binary systems. Active M dwarfs are likely present in 155 Balmer-emitting systems, corresponding to a fraction of 24.4 %. The excess of cool DOs is most likely due to additional WDs in the DB-DO T_eff range, for which no detailed fitting was completed. The trend of the M stars being closer to Earth than the WD component is probably due to an underestimation of the theoretical M star radii.Comment: accepted by A&A October 3, 2008, 15 pages, 16 figures, 3 tables; v2, minor grammatical changes, essential changes in Sect. 5.

Development of material specifications and qualifications of polymeric materials for the jpl spacecraft materials guide book. iii- polyfluorocarbon films special report no. 3

Outgassing studies of polyfluorocarbon films - investigation of polymers as spacecraft construction material

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