Abstract: In various embodiments of an analytics system, a spike-in including synthetic constructs of nucleic acid is added to soil samples for processing. The analytics system determines sequence reads classified to a microbe in the soil sample. The analytics system determines one or more measures of soil texture of the soil sample, for example, indicating percentages of sand, silt, and clay. The analytics system determines a measure of the microbe as a function of at least the classified sequence reads, the one or more measures of soil texture, and a mass of the spike-in. The analytics system can transmit the measure of the microbe to a client device for display on a user interface. A field where the soil sample was obtained can be treated according to the measure of the microbe.

Abstract: An analytics system uses soil health indicators to determine metrics for soil samples. In an embodiment, the analytics system receives metadata describing a soil sample, where the metadata indicates one or more types of crops grown in a geographical location having the soil sample. The analytics system determines nucleic acid sequence reads of the soil sample. The analytics system determines taxonomic information of the nucleic acid sequence reads. The analytics system determines microbial composition of the soil sample using the taxonomic information. The analytics system determines reference metrics of soil samples from geographical locations in which the one or more types of crop were grown. The analytics system determines a metric of the soil sample using the microbial composition and the reference metrics. The analytics system transmits the metric to a client device.

Abstract: A method of indicating a characteristic of a soil sample of a field includes measuring a co-factor in the soil sample and using the co-factor to place the soil sample in a soil sample group. The characteristic of the soil sample is measured and then is scaled based on the soil sample group. The scaled measure is displayed to better represent the characteristic of the soil sample relative to soil samples of the sample group.

Abstract: An analytics system uses soil health indicators to determine metrics for soil samples. In an embodiment, the analytics system receives metadata describing a soil sample, where the metadata indicates one or more types of crops grown in a geographical location having the soil sample. The analytics system determines nucleic acid sequence reads of the soil sample. The analytics system determines taxonomic information of the nucleic acid sequence reads. The analytics system determines microbial composition of the soil sample using the taxonomic information. The analytics system determines reference metrics of soil samples from geographical locations in which the one or more types of crop were grown. The analytics system determines a metric of the soil sample using the microbial composition and the reference metrics. The analytics system transmits the metric to a client device.

Abstract: An analytics system uses metagenomics to generate predictions indicating performance of biological or physical samples. In an embodiment, a method includes determining sequence data of a soil sample. The method further includes determining a plurality of features of the soil sample using the sequence data. The plurality of features is determined based at least in part on a measure of a first microbe detected in the soil sample and a different measure of a second microbe detected in the soil sample. The method further includes inputting the plurality of features to a model trained using measures of the first microbe and the second microbe detected in a plurality of soil samples. The method further includes generating, by the model using the plurality of features, a prediction of physical attribute of a plant grown in the soil sample.

Abstract: In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.

Abstract: The present disclosure relates to the profiling of microorganisms in an environmental sample. Specifically, the present disclosure relates to methods of using molecular inversion probes comprising unique molecular identifiers to profile microorganisms in an environmental sample. In addition, the present disclosure relates to compositions of molecular inversion probes comprising unique molecular identifiers to profile microorganisms in an environmental sample.

Abstract: A system and method for the detection of pathogens and other microbes using nucleotide analysis is described. Aligned and unaligned nucleotide sequences are utilized to predict the presence or absence of pathogens and other microbes.

Abstract: Methods for quantifying the efficiency of nucleic acid extraction from a sample comprising a mixture of species are provided. In some embodiments, the method comprises adding an initial amount of one or more spike-ins to the sample, extracting nucleic acids from the sample, quantifying the amount of the one or more spike-ins in the extracted nucleic acid sample, and comparing the initial amount of the one or more spike-ins to the quantified amount of the one or more spike-ins.