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Data from: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

    We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly.

    Data from: United States wildlife and wildlife product imports from 2000–2014

      Data are presented on 15 years of the importation of wildlife and their derived products into the United States (2000–2014), originally collected by the United States Fish and Wildlife Service. These data include >2 million wildlife or wildlife product shipments, representing >60 biological classes and >3.2 billion live organisms. The data were curated and cleaned, and taxonomic information added to improve usability.

      Breedbase

        The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org).Breedbase is striving to be a complete breeding management system, including field management, data collection, crossing utilities, and advanced trial analysis.

        Economic Model of Deficit Irrigation

          The model calculates net income from a crop on a unit of land based on a quadratic crop water production function, amount of effective precipitation, irrigation efficiency, cost of the irrigation water supply, crop production costs, and revenue from selling the crop. The model includes potential income from leasing out saved irrigation water. All biophysical variables are defined in terms of the relative evapotranspiration. Net income is maximized by optimizing the amount of water consumed by the crop.

          Soil Texture Calculator

            The Soil Texture Calculator web tool allows the user to input sand and clay percentages to obtain the soil texture. An Excel version is also available for download.

            sharpshootR: A Soil Survey Toolkit

              Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey operations within the USDA-NRCS. Many of the functions are highly specialized and inherit default arguments from the names used by the various NCSS (National Cooperative Soil Survey) databases.

              soilDB: Soil Database Interface

                soilDB is one of the Algorithms for Quantitative Pedology (AQP) suite of R packages, and comprises a collection of functions for reading data from USDA-NCSS soil databases including SoilWeb, Series Extent Explorer, and Soil Data Explorer.

                Algorithms for Quantitative Pedology (AQP)

                  Algorithms for Quantitative Pedology (AQP) is a collection of code, ideas, documentation, and examples wrapped-up into several R packages. The AQP suite of R packages are used to generate figures for SoilWeb, Series Extent Explorer, and Soil Data Explorer.