Long reads: their purpose and place.

In recent years long-read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing, the cost of sequencing using long-read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterizing genomes at high resolution. In this article, we will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics

Twelve years of SAMtools and BCFtools.

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org

A systematic fitting scheme for caustic-crossing microlensing events

We outline a method for fitting binary-lens caustic-crossing microlensing events based on the alternative model parameterisation proposed and detailed in Cassan (2008). As an illustration of our methodology, we present an analysis of OGLE-2007-BLG-472, a double-peaked Galactic microlensing event with a source crossing the whole caustic structure in less than three days. In order to identify all possible models we conduct an extensive search of the parameter space, followed by a refinement of the parameters with a Markov Chain-Monte Carlo algorithm. We find a number of low-chi2 regions in the parameter space, which lead to several distinct competitive best models. We examine the parameters for each of them, and estimate their physical properties. We find that our fitting strategy locates several minima that are difficult to find with other modelling strategies and is therefore a more appropriate method to fit this type of events.Comment: 12 pages, 11 figure

Limb-darkening measurements for a cool red giant in microlensing event OGLE 2004-BLG-482

Aims: We present a detailed analysis of OGLE 2004-BLG-482, a relatively high-magnification single-lens microlensing event which exhibits clear extended-source effects. These events are relatively rare, but they potentially contain unique information on the stellar atmosphere properties of their source star, as shown in this study. Methods: Our dense photometric coverage of the overall light curve and a proper microlensing modelling allow us to derive measurements of the OGLE 2004-BLG-482 source star's linear limb-darkening coefficients in three bands, including standard Johnson-Cousins I and R, as well as in a broad clear filter. In particular, we discuss in detail the problems of multi-band and multi-site modelling on the expected precision of our results. We also obtained high-resolution UVES spectra as part of a ToO programme at ESO VLT from which we derive the source star's precise fundamental parameters. Results: From the high-resolution UVES spectra, we find that OGLE 2004-BLG-482's source star is a red giant of MK type a bit later than M3, with Teff = 3667 +/- 150 K, log g = 2.1 +/- 1.0 and an assumed solar metallicity. This is confirmed by an OGLE calibrated colour-magnitude diagram. We then obtain from a detailed microlensing modelling of the light curve linear limb-darkening coefficients that we compare to model-atmosphere predictions available in the literature, and find a very good agreement for the I and R bands. In addition, we perform a similar analysis using an alternative description of limb darkening based on a principal component analysis of ATLAS limb-darkening profiles, and also find a very good agreement between measurements and model predictions.Comment: Accepted in A&

Les Houches 2015: Physics at TeV colliders - new physics working group report

We present the activities of the 'New Physics' working group for the 'Physics at TeV Colliders' workshop (Les Houches, France, 1-19 June, 2015). Our report includes new physics studies connected with the Higgs boson and its properties, direct search strategies, reinterpretation of the LHC results in the building of viable models and new computational tool developments. Important signatures for searches for natural new physics at the LHC and new assessments of the interplay between direct dark matter searches and the LHC are also considered.Comment: Proceedings of the New Physics Working Group of the 2015 Les Houches Workshop, Physics at TeV Colliders, Les Houches 1-19 June 2015. 197 page

OGLE-2005-BLG-153: Microlensing Discovery and Characterization of A Very Low Mass Binary

The mass function and statistics of binaries provide important diagnostics of the star formation process. Despite this importance, the mass function at low masses remains poorly known due to observational difficulties caused by the faintness of the objects. Here we report the microlensing discovery and characterization of a binary lens composed of very low-mass stars just above the hydrogen-burning limit. From the combined measurements of the Einstein radius and microlens parallax, we measure the masses of the binary components of $0.10\pm 0.01\ M_\odot$ and $0.09\pm 0.01\ M_\odot$. This discovery demonstrates that microlensing will provide a method to measure the mass function of all Galactic populations of very low mass binaries that is independent of the biases caused by the luminosity of the population.Comment: 6 pages, 3 figures, 1 tabl

OGLE-2005-BLG-071Lb, the Most Massive M-Dwarf Planetary Companion?

We combine all available information to constrain the nature of OGLE-2005-BLG-071Lb, the second planet discovered by microlensing and the first in a high-magnification event. These include photometric and astrometric measurements from Hubble Space Telescope, as well as constraints from higher order effects extracted from the ground-based light curve, such as microlens parallax, planetary orbital motion and finite-source effects. Our primary analysis leads to the conclusion that the host of Jovian planet OGLE-2005-BLG-071Lb is an M dwarf in the foreground disk with mass M= 0.46 +/- 0.04 Msun, distance D_l = 3.3 +/- 0.4 kpc, and thick-disk kinematics v_LSR ~ 103 km/s. From the best-fit model, the planet has mass M_p = 3.8 +/- 0.4 M_Jup, lies at a projected separation r_perp = 3.6 +/- 0.2 AU from its host and so has an equilibrium temperature of T ~ 55 K, i.e., similar to Neptune. A degenerate model less favored by \Delta\chi^2 = 2.1 (or 2.2, depending on the sign of the impact parameter) gives similar planetary mass M_p = 3.4 +/- 0.4 M_Jup with a smaller projected separation, r_\perp = 2.1 +/- 0.1 AU, and higher equilibrium temperature T ~ 71 K. These results from the primary analysis suggest that OGLE-2005-BLG-071Lb is likely to be the most massive planet yet discovered that is hosted by an M dwarf. However, the formation of such high-mass planetary companions in the outer regions of M-dwarf planetary systems is predicted to be unlikely within the core-accretion scenario. There are a number of caveats to this primary analysis, which assumes (based on real but limited evidence) that the unlensed light coincident with the source is actually due to the lens, that is, the planetary host. However, these caveats could mostly be resolved by a single astrometric measurement a few years after the event.Comment: 51 pages, 12 figures, 3 tables, Published in Ap

Combined Analysis of the Binary-Lens Caustic-Crossing Event MACHO 98-SMC-1

We fit the data for the binary-lens microlensing event MACHO 98-SMC-1 from 5 different microlensing collaborations and find two distinct solutions characterized by binary separation d and mass ratio q: (d,q)=(0.54,0.50) and (d,q)=(3.65,0.36), where d is in units of the Einstein radius. However, the relative proper motion of the lens is very similar in the two solutions, 1.30 km/s/kpc and 1.48 km/s/kpc, thus confirming that the lens is in the Small Magellanic Cloud. The close binary can be either rotating or approximately static but the wide binary must be rotating at close its maximum allowed rate to be consistent with all the data. We measure limb-darkening coefficients for five bands ranging from I to V. As expected, these progressively decrease with rising wavelength. This is the first measurement of limb darkening for a metal-poor A star.Comment: 29 pages + 9 figures + 2 tables, submitted to Ap

Interpretation of Strong Short-Term Central Perturbations in the Light Curves of Moderate-Magnification Microlensing Events

To improve the planet detection efficiency, current planetary microlensing experiments are focused on high-magnification events searching for planetary signals near the peak of lensing light curves. However, it is known that central perturbations can also be produced by binary companions and thus it is important to distinguish planetary signals from those induced by binary companions. In this paper, we analyze the light curves of microlensing events OGLE-2007-BLG-137/MOA-2007-BLG-091, OGLE-2007-BLG-355/MOA-2007-BLG-278, and MOA-2007-BLG-199/OGLE-2007-BLG-419, for all of which exhibit short-term perturbations near the peaks of the light curves. From detailed modeling of the light curves, we find that the perturbations of the events are caused by binary companions rather than planets. From close examination of the light curves combined with the underlying physical geometry of the lens system obtained from modeling, we find that the short time-scale caustic-crossing feature occurring at a low or a moderate base magnification with an additional secondary perturbation is a typical feature of binary-lens events and thus can be used for the discrimination between the binary and planetary interpretations.Comment: 17 pages, 4 figures, 1 tabl

Frequency of Solar-Like Systems and of Ice and Gas Giants Beyond the Snow Line from High-Magnification Microlensing Events in 2005-2008

We present the first measurement of planet frequency beyond the "snow line" for planet/star mass-ratios[-4.5<log q<-2]: d^2 N/dlog q/dlog s=(0.36+-0.15)/dex^2 at mean mass ratio q=5e-4, and consistent with being flat in log projected separation, s. Our result is based on a sample of 6 planets detected from intensive follow-up of high-mag (A>200) microlensing events during 2005-8. The sample host stars have typical mass M_host 0.5 Msun, and detection is sensitive to planets over a range of projected separations (R_E/s_max,R_E*s_max), where R_E 3.5 AU sqrt(M_host/Msun) is the Einstein radius and s_max (q/5e-5)^{2/3}, corresponding to deprojected separations ~3 times the "snow line". Though frenetic, the observations constitute a "controlled experiment", which permits measurement of absolute planet frequency. High-mag events are rare, but the high-mag channel is efficient: half of high-mag events were successfully monitored and half of these yielded planet detections. The planet frequency derived from microlensing is a factor 7 larger than from RV studies at factor ~25 smaller separations [2<P<2000 days]. However, this difference is basically consistent with the gradient derived from RV studies (when extrapolated well beyond the separations from which it is measured). This suggests a universal separation distribution across 2 dex in semi-major axis, 2 dex in mass ratio, and 0.3 dex in host mass. Finally, if all planetary systems were "analogs" of the Solar System, our sample would have yielded 18.2 planets (11.4 "Jupiters", 6.4 "Saturns", 0.3 "Uranuses", 0.2 "Neptunes") including 6.1 systems with 2 or more planet detections. This compares to 6 planets including one 2-planet system in the actual sample, implying a first estimate of 1/6 for the frequency of solar-like systems.Comment: 42 pages, 10 figure