Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.

The ATLAS IBL CollaborationDuring the shutdown of the CERN Large Hadron Collider in 2013-2014, an additional pixel layer was installed between the existing Pixel detector of the ATLAS experiment and a new, smaller radius beam pipe. The motivation for this new pixel layer, the Insertable B-Layer (IBL), was to maintain or improve the robustness and performance of the ATLAS tracking system, given the higher instantaneous and integrated luminosities realised following the shutdown. Because of the extreme radiation and collision rate environment, several new radiation-tolerant sensor and electronic technologies were utilised for this layer. This paper reports on the IBL construction and integration prior to its operation in the ATLAS detector.The ATLAS [1] general purpose detector is used for the study of proton-proton (pp) and heavy-ion collisions at the CERN Large Hadron Collider (LHC) [2]. It successfully collected data at pp collision energies of 7 and 8 TeV in the period of 2010-2012, known as Run 1. Following an LHC shutdown in 2013-2014 (LS1), it has collected data since 2015 at a pp collision energy of 13 TeV (the so-called Run 2).The ATLAS inner tracking detector (ID) [1, 3] provides charged particle tracking with high efficiency in the pseudorapidity 1 range of |η| < 2.5. With increasing radial distance from the interaction region, it consists of silicon pixel and micro-strip detectors, followed by a transition radiation tracker (TRT) detector, all surrounded by a superconducting solenoid providing a 2 T magnetic field.The original ATLAS pixel detector [4,5], referred to in this paper as the Pixel detector, was the innermost part of the ID during Run 1. It consists of three barrel layers (named the B-Layer, Layer 1 and Layer 2 with increasing radius) and three disks on each side of the interaction region, to guarantee at least three space points over the full tracking |η| range. It was designed to operate for the Phase-I period of the LHC, that is with a peak luminosity of 1 × 10 34 cm −2 s −1 and an integrated luminosity of approximately 340 fb −1 corresponding to a TID of up to 50 MRad 2 and a fluence of up to 1 × 10 15 n eq /cm 2 NIEL. However, for luminosities exceeding 2 × 10 34 cm −2 s −1 , which are now expected during the Phase-I operation, the read-out efficiency of the Pixel layers will deteriorate. This paper describes the construction and surface integration of an additional pixel layer, the Insertable B-Layer (IBL) [6], installed during the LS1 shutdown between the B-Layer and a new smaller radius beam pipe. The main motivations of the IBL were to maintain the full ID tracking performance and robustness during Phase-I operation, despite read-out bandwidth limitations of the Pixel layers (in particular the B-Layer) at the expected Phase-I peak luminosity, and accumulated radiation damage to the silicon sensors and front-end electronics. The IBL is designed to operate until the end of Phase-I, when a full tracker upgrade is planned [7] for high luminosity LHC (HL-LHC) operation from approximately ...

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The ATLAS luminosity monitor, LUCID (LUminosity Cherenkov Integrating Detector), had to be upgraded for the second run of the LHC accelerator that started in spring 2015. The increased energy of the proton beams and the higher luminosity required a redesign of LUCID to cope with the more demanding conditions. The novelty of the LUCID-2 detector is that it uses the thin quartz windows of photomultipliers as Cherenkov medium and a small amounts of radioactive 207 Bi sources deposited on to these windows to monitor the gain stability of the photomultipliers.The result is a fast and accurate luminosity determination that can be kept stable during many months of data taking. LUCID-2 can also measure the luminosity accurately online for each of the up to 2808 colliding bunch pairs in the LHC. These bunch pairs are separated by only 25 ns and new electronics has been built that can count not only the number of pulses above threshold but also integrate the pulses. K: Cherenkov detectors; Photon detectors for UV, visible and IR photons (vacuum) (photomultipliers, HPDs, others) 1Corresponding author.