Abstract: The disclosed embodiments concern methods for designing probes for improving environmental sample (including wastewater samples and other samples) surveillance and surveillance of other samples for various viruses. In certain embodiments described herein, methods and systems are provided for designing a pool of probes for enriching a sample for one or more target viral nucleic acids.

Abstract: Described herein are compositions and methods for enriching library fragments comprising viral sequences prepared from a variety of samples. These methods may incorporate microfluidics and flowcells for greater ease of use. Libraries enriched with the present methods may be used for sequencing. Also described are probes and methods for enzymatic depletion of unwanted RNA.

Abstract: Systems and methods for determining an amount of a predefined category are provided. A sample is obtained, including nucleic acids from the predefined category and nucleic acids from a source other than the predefined category. A known quantity of an internal control material comprising nucleic acids is added to the sample. The sample, including the internal control material, is sequenced. A sequencing dataset including sequence reads from the predefined category and sequence reads from the internal control material is obtained. A first read count, normalized using a first target nucleotide length, of sequence reads from the predefined category, and a second read count, normalized using a second target nucleotide length, of sequence reads from the internal control material are determined. The amount of the predefined category in the sample is calculated based on the first read count, the second read count, and the known quantity of the internal control material.

Abstract: A method for reviewing sequencing data for identifying microorganisms in a sample is provided. A request to display an analysis of a result set obtained from sequencing nucleic acids from the sample is received. The result set includes sequencing statistics, nucleotide sequences mapped against microorganism reference sequences, and mapping statistics for the mapping of nucleotide sequences to each respective reference sequence. A first customizable diagnostic template is applied to the result set. The customizable diagnostic template specifies a subset of sequencing statistics, a subset of microorganisms, and a subset of mapping statistics. A customizable user interface is displayed comprising a. review' status, a.