WebQUAST: online evaluation of genome assemblies

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it

Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer

The value of high-throughput germline genetic testing is increasingly recognized inclinical cancer care. Disease-associated germline variants in cancer patients areimportant for risk management and surveillance, surgical decisions and can also havemajor implications for treatment strategies since many are in DNA repair genes. Withthe increasing availability of high-throughput DNA sequencing in cancer clinics andresearch, there is thus a need to provide clinically oriented sequencing reports forgermline variants and their potential therapeutic relevance on a per-patient basis. Tomeet this need, we have developed the Cancer Predisposition Sequencing Reporter(CPSR), an open-source computational workflow that generates a structured reportof germline variants identified in known cancer predisposition genes, highlightingmarkers of therapeutic, prognostic and diagnostic relevance. A fully automated vari-ant classification procedure based on more than 30 refined American College ofMedical Genetics and Genomics (ACMG) criteria represents an integral part of theworkflow. Importantly, the set of cancer predisposition genes profiled in the reportcan be flexibly chosen from more than 40 virtual gene panels established by scientificexperts, enabling customization of the report for different screening purposes andclinical contexts. The report can be configured to also list actionable secondary vari-ant findings, as recommended by ACMG. CPSR demonstrates comparable sensitivityand specificity for the detection of pathogenic variants when compared to otheralgorithms in the field. Technically, the tool is implemented in Python/R, and is freelyavailable through Docker technology. Source code, documentation, example reportsand installation instructions are accessible via the project GitHub page: https://github.com/sigven/cpsr.publishedVersio

Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer

The value of high-throughput germline genetic testing is increasingly recognized inclinical cancer care. Disease-associated germline variants in cancer patients areimportant for risk management and surveillance, surgical decisions and can also havemajor implications for treatment strategies since many are in DNA repair genes. Withthe increasing availability of high-throughput DNA sequencing in cancer clinics andresearch, there is thus a need to provide clinically oriented sequencing reports forgermline variants and their potential therapeutic relevance on a per-patient basis. Tomeet this need, we have developed the Cancer Predisposition Sequencing Reporter(CPSR), an open-source computational workflow that generates a structured reportof germline variants identified in known cancer predisposition genes, highlightingmarkers of therapeutic, prognostic and diagnostic relevance. A fully automated vari-ant classification procedure based on more than 30 refined American College ofMedical Genetics and Genomics (ACMG) criteria represents an integral part of theworkflow. Importantly, the set of cancer predisposition genes profiled in the reportcan be flexibly chosen from more than 40 virtual gene panels established by scientificexperts, enabling customization of the report for different screening purposes andclinical contexts. The report can be configured to also list actionable secondary vari-ant findings, as recommended by ACMG. CPSR demonstrates comparable sensitivityand specificity for the detection of pathogenic variants when compared to otheralgorithms in the field. Technically, the tool is implemented in Python/R, and is freelyavailable through Docker technology. Source code, documentation, example reportsand installation instructions are accessible via the project GitHub page: https://github.com/sigven/cpsr

International Large Detector: Interim Design Report

The ILD detector is proposed for an electron-positron collider with collision centre-of-mass energies from 90~\GeV~to about 1~\TeV. It has been developed over the last 10 years by an international team of scientists with the goal to design and eventually propose a fully integrated detector, primarily for the International Linear Collider, ILC. In this report the fundamental ideas and concepts behind the ILD detector are discussed and the technologies needed for the realisation of the detector are reviewed. The document starts with a short review of the science goals of the ILC, and how the goals can be achieved today with the detector technologies at hand. After a discussion of the ILC and the environment in which the experiment will take place, the detector is described in more detail, including the status of the development of the technologies foreseen for each subdetector. The integration of the different sub-systems into an integrated detector is discussed, as is the interface between the detector and the collider. This is followed by a concise summary of the benchmarking which has been performed in order to find an optimal balance between performance and cost. To the end the costing methodology used by ILD is presented, and an updated cost estimate for the detector is presented. The report closes with a summary of the current status and of planned future actions

The ILD detector at the ILC

The International Large Detector, ILD, is a detector concept which has been developed for the electron-positron collider ILC. The detector has been optimized for precision physics in a range of energies between 90 GeV and 1 TeV. ILD features a high precision, large volume combined silicon and gaseous tracking system, together with a high granularity calorimeter, all inside a 3.5 T solenoidal magnetic field. The paradigm of particle flow has been the guiding principle of the design of ILD. In this document the required performance of the detector, the proposed implementation and the readiness of the different technologies needed for the implementation are discussed. This is done in the framework of the ILC collider proposal, now under consideration in Japan, and includes site specific aspects needed to build and operate the detector at the proposed ILC site in Japan

Tevatron Combination of Single-Top-Quark Cross Sections and Determination of the Magnitude of the Cabibbo-Kobayashi-Maskawa Matrix Element Vtb\bf V_{tb}

We present the final combination of CDF and D0 measurements of cross sections for single-top-quark production in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. The data correspond to total integrated luminosities of up to 9.7 fb$^{−1}$ per experiment. The t-channel cross section is measured to be σ$_t$=2.25$_{-0.31}^{+0.29}$ pb. We also present the combinations of the two-dimensional measurements of the s- vs t-channel cross section. In addition, we give the combination of the s+t channel cross section measurement resulting in σ$_{s+t}$=3.30$_{-0.40}^{+0.52}$ pb, without assuming the standard model value for the ratio σ$_s$/σ$_t$. The resulting value of the magnitude of the top-to-bottom quark coupling is |V$_{tb}$|=1.02$_{-0.05}^{+0.06}$, corresponding to |V$_{tb}$|>0.92 at the 95% C.L

Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron

International audienceThe CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of s=1.96  TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is AFBtt¯=0.128±0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions

Tevatron Run II combination of the effective leptonic electroweak mixing angle

International audienceDrell-Yan lepton pairs produced in the process pp¯→ℓ+ℓ-+X through an intermediate γ*/Z boson have an asymmetry in their angular distribution related to the spontaneous symmetry breaking of the electroweak force and the associated mixing of its neutral gauge bosons. The CDF and D0 experiments have measured the effective-leptonic electroweak mixing parameter sin2θefflept using electron and muon pairs selected from the full Tevatron proton-antiproton data sets collected in 2001-2011, corresponding to 9–10  fb-1 of integrated luminosity. The combination of these measurements yields the most precise result from hadron colliders, sin2θefflept=0.23148±0.00033. This result is consistent with, and approaches in precision, the best measurements from electron-positron colliders. The standard model inference of the on-shell electroweak mixing parameter sin2θW, or equivalently the W-boson mass MW, using the zfitter software package yields sin2θW=0.22324±0.00033 or equivalently, MW=80.367±0.017  GeV/c2