Primary analysis in next generation sequencing

A system comprising:

• one or more hardware processors;
• one or more data storage devices storing instructions executable by the one or more hardware processors that, when executed, cause the one or more hardware processors to perform operations, the operations comprising:
• generating, by a sequencing system, a first plurality of flow cell images of a cellular sample immobilized on a support by conducting one or more cycles of sequencing reactions, the cellular sample comprising a plurality of concatemer molecules therewithin, wherein a first concatemer molecule of the plurality of concatemer molecules corresponds to a first target RNA molecule of the cellular sample, and a second concatemer molecule of the plurality of concatemer molecules corresponds to a second target RNA molecule of the cellular sample;
• determining, by a processor, for pixels of the first plurality of flow cell image, pixel intensities and a respective color purity of each of the pixel intensities;
• and
• determining, by the processor and based on the pixel intensities and the respective color purity of the pixel intensities, a base calling template comprising base calling locations, wherein the base calling template is configured for registering a second plurality of flow cell images of the cellular sample in one or more subsequent cycles of the one or more cycles.

One or more non-transitory computer storage media encoded with instructions executable by one or more hardware processors that, when executed, cause the one or more hardware processors to perform operations, the operations comprising:

• generating, by a sequencing system, a first plurality of flow cell images of a cellular sample immobilized on a support by conducting one or more cycles of sequencing reactions, the cellular sample comprising a plurality of concatemer molecules therewithin, wherein a first concatemer molecule of the plurality of concatemer molecules corresponds to a first target RNA molecule of the cellular sample, and a second concatemer molecule of the plurality of concatemer molecules corresponds to a second target RNA molecule of the cellular sample;
• determining, by a processor, for pixels of the first plurality of flow cell image, pixel intensities and a respective color purity of each of the pixel intensities;
• and
• determining, by the processor and based on the pixel intensities and the respective color purity of the pixel intensities, a base calling template comprising base calling locations, wherein the base calling template is configured for registering a second plurality of flow cell images of the cellular sample in one or more subsequent cycles of the one or more cycles.