Abstract: Provided herein are methods for aligning raw genetic sequence data generated by a sequencing device. Also provided herein are methods and systems for quantifying the probability that possible alignments for one or more read pairs are correct, for calling known variants, and for detecting novel structural variants.

Abstract: In accordance with some embodiments, systems, methods, and media for classifying genetic sequencing results based on pathogen-specific adaptive thresholds are provided. In some embodiments, a system comprises a processor programmed to: receive negative control results, each comprising values indicative of a number of reads detected in the respective negative control sample for an organism; generate a model based on the negative control results; receive a clinical sample result for a clinical sample, comprising values indicative of a number of reads detected in the clinical sample for an organism of a plurality of organisms; identify, utilizing the model, any values in the clinical sample that are likely to be diagnostically significant; generate a report based on the clinical sample result and organisms associated with a value likely to be diagnostically significant; and cause the report to be presented to a user.

Abstract: In accordance with some embodiments, systems, methods, and media for determining relative quality of oligonucleotide preparations. In some embodiments, a system comprises a processor programmed to: (a) receive genetic sequencing results for multiple libraries with target concentrations of oligonucleotides; (b) calculate at least one prediction band; (c) repeat (a) and (b) for multiple preparations; (d) determine boundaries for a final prediction band based on the prediction bands calculated at (b) for each of the preparations; and (e) present a report indicative of quality of the libraries, including metrics indicative of the final prediction band.

Abstract: A device for compressing subject data. the device comprises a communication link, the communication link capable of receiving a set of subject data; a compression module, the compression module configured to apply a compression algorithm to the set of subject data, the compression algorithm compressing the set of subject data using a reference string of subject data; and a transmission module, the transmission module configured to transmit the compressed subject data. The device further comprising an encryption module for encrypting the subject data.

Abstract: Provided herein are methods for aligning raw genetic sequence data generated by a sequencing device. Also provided herein are methods and systems for quantifying the probability that possible alignments for one or more read pairs are correct, for calling known variants, and for detecting novel structural variants.

Abstract: A device for compressing subject data, the device comprises a communication link, the communication link capable of receiving a set of subject data; a compression module, the compression module configured to apply a compression algorithm to the set of subject data, the compression algorithm compressing the set of subject data using a reference string of subject data; and a transmission module, the transmission module configured to transmit the compressed subject data. The device further comprising an encryption module for encrypting the subject data.