Abstract: Exemplary embodiments for a multiprocessor pipeline architecture that converts signals from sequencing sample acquisition into sequence data, comprising: a custom coprocessor card configured to directly receive a stream of serialized sensor data generated by an image sensor, wherein the sensor data represents frame-by-frame intensity values for pixels comprising the image sensor, wherein the image sensor captures images of light emitted from a plurality of reaction cells of a removable integrated sequencing chip; a first coprocessor that continually receives the stream of serialized sensor data and transposes the frame-by-frame intensity values into reaction cell chunks, each of the reaction cell chunks representing movie data of the pixel intensity values of a corresponding reaction cell across the frames over a predetermined time window; a buffer that repeatedly receives the reaction cell chunks and stores in contiguous memory locations the reaction cell chunks for each respective reaction cell over a large

Abstract: Methods and systems for obtaining and processing optical signal data from analytical reactions, and in processing signal data from arrays of sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof are described. Defining and applying a 2-dimensional software mask allows for obtaining signal data from arrays with higher signal to noise than where the mask is not applied.

Abstract: A system performs two types of spectral calibration. For the first type, the system collects data from monitoring an analytical separation of several spectrally-distinguishable molecular species and creates a data matrix from the collected data. Each element in the data matrix represents a signal intensity at a particular time and over a particular range of light wavelengths. The system then identifies regions in the data matrix that have spectral response characteristics of at least one of the molecular species, determines a set of pure component spectral responses from the identified regions, groups similar pure component spectral responses into clusters, determines a representative spectral response for each cluster, and correlates the representative spectral response for each cluster with one of the molecular species.