MOTIVATION: Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accuracy, long-read sequencing can substantially improve SV characterization when coupled with effective calling methods. While state-of-the-art long-read SV callers are highly accurate, further improvements are achievable by systematically modeling local haplotypes during SV discovery and genotyping. RESULTS: We describe sawfish, an SV caller for mapped high-quality long reads incorporating systematic SV haplotype modeling to improve accuracy and resolution. Assessment against the draft Genome in a Bottle (GIAB) SV benchmark from the T2T-HG002-Q100 diploid assembly shows that sawfish has the highest accuracy among state-of-the-art long-read SV callers across every tested SV size group. Additionally, sawfish maintains the highest accuracy at every tested depth level from 10- to 32-fold coverage, such that other callers required at least 30-fold coverage to match sawfish accuracy at 15-fold coverage. Sawfish also shows the highest accuracy in the GIAB challenging medically relevant genes benchmark, demonstrating improvements in both comprehensive and medically relevant contexts.When joint-genotyping seven samples from CEPH-1463, sawfish has over 9000 more pedigree-concordant calls than other state-of-the-art SV callers, with the highest proportion of concordant SVs (81%). Sawfish's quality model enables selection for an even higher proportion of concordant SVs (88%), while still calling nearly 5000 more pedigree-concordant SVs than other callers. These results demonstrate that sawfish improves on the state-of-the-art for long-read SV calling accuracy across both individual and joint-sample analyses. AVAILABILITY AND IMPLEMENTATION: Sawfish source code, pre-compiled Linux binaries, and documentation are released on GitHub: https://github.com/PacificBiosciences/sawfish.

MOTIVATION: A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can be slow and can require different tools for different input file types. RESULTS: Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package. AVAILABILITY AND IMPLEMENTATION: https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We initiate the study of coresets for clustering in graph metrics, i.e., the shortest-path metric of edge-weighted graphs. Such clustering problems are essential to data analysis and used for example in road networks and data visualization. A coreset is a compact summary of the data that approximately preserves the clustering objective for every possible center set, and it offers significant efficiency improvements in terms of running time, storage, and communication, including in streaming and distributed settings. Our main result is a near-linear time construction of a coreset for k-Median in a general graph $G$, with size $O_{\epsilon, k}(\mathrm{tw}(G))$ where $\mathrm{tw}(G)$ is the treewidth of $G$, and we complement the construction with a nearly-tight size lower bound. The construction is based on the framework of Feldman and Langberg [STOC 2011], and our main technical contribution, as required by this framework, is a uniform bound of $O(\mathrm{tw}(G))$ on the shattering dimension under any point weights. We validate our coreset on real-world road networks, and our scalable algorithm constructs tiny coresets with high accuracy, which translates to a massive speedup of existing approximation algorithms such as local search for graph k-Median.

The scientific objectives of the NASA small-class explorer mission SAMPEX are summarized. A brief history of the Small Explorer Program is provided along with a description of the SAMPEX project development and structure. The spacecraft and scientific instrument configuration is presented. The orbit of SAMPEX has an altitude of 520 by 670 km and an 82 degrees inclination. Maximum possible power is provided by articulated solar arrays that point continuously toward the sun. Highly sensitive scientific instruments point generally toward the local zenith, especially over the terrestrial poles, in order to measure optimally the galactic and solar cosmic ray flux. Energetic magnetospheric particle precipitation is monitored at lower geomagnetic latitudes. The spacecraft uses several innovative approaches including an optical fiber bus, powerful onboard computers, and large solid state memories (instead of tape recorders). Spacecraft communication and data acquisition are discussed and the space- and ground-segment data flows are summarized.>

The proton/electron telescope (PET) on SAMPEX (Solar, Anomalous, and Magnetospheric Particle Explorer) is designed to provide measurements of energetic electrons and light nuclei from solar, Galactic, and magnetospheric sources. PET is an all solid-state system that will measure the differential energy spectra of electrons from approximately 1 to approximately 30 MeV and H and He nuclei from approximately 20 to approximately 300 MeV/nucleon, with isotope resolution of H and He extending from approximately 20 to approximately 80 MeV/nucleon. As SAMPEX scans all local times and geomagnetic cutoffs over the course of its near-polar orbit, PET will characterize precipitating relativistic electron events during periods of declining solar activity, and it will examine whether the production rate of odd nitrogen and hydrogen molecules in the middle atmosphere by precipitating electrons is sufficient to affect O/sub 3/ depletion. In addition, PET will complement studies of the elemental and isotopic composition of energetic heavy (Z>2) nuclei on SAMPEX by providing measurements of H, He, and electrons. Finally, PET has limited capability to identify energetic positrons from potential natural and man-made sources.>