Base calling using three-dimentional (3d) convolution

A non-transitory computer readable storage medium impressed with computer program instructions to base call analytes, the instructions, when executed on a processor, implement a method comprising:

• accessing a sequence of per-cycle image patches generated for a series of sequencing cycles of a sequencing run, wherein pixels in the per-cycle image patches contain intensity data for associated analytes in one or more imaged channels;
• applying three-dimensional (3D) convolutions on the sequence of per-cycle image patches on a sliding convolution window basis such that, in a convolution window, a 3D convolution filter convolves over a plurality of the per-cycle image patches and produces at least one output feature as a result of convolving over the sequence of per-cycle image patches on the sliding convolution window basis;
• beginning with output features produced by the 3D convolutions as starting input, applying further convolutions and producing final output features;
• and
• processing the final output features through an output layer and producing base calls for one or more of the associated analytes to be base called at each of the sequencing cycles.

A system including one or more processors coupled to memory, the memory loaded with computer instructions to base call analytes, the instructions, when executed on the processors, implement actions comprising:

• accessing a sequence of per-cycle image patches generated for a series of sequencing cycles of a sequencing run, wherein pixels in the per-cycle image patches contain intensity data for associated analytes in one or more imaged channels;
• applying three-dimensional (3D) convolutions on the sequence of per-cycle image patches on a sliding convolution window basis such that, in a convolution window, a 3D convolution filter convolves over a plurality of the per-cycle image patches and produces at least one output feature as a result of convolving over the sequence of per-cycle image patches on the sliding convolution window basis;
• beginning with output features produced by the 3D convolutions as starting input, applying further convolutions and producing final output features;
• and
• processing the final output features through an output layer and producing base calls for one or more of the associated analytes to be base called at each of the sequencing cycles.