A method for determining a sequence of a target nucleic acid, the method comprising performing by a computer system: for each control partition of a plurality of control partitions, each control partition including a plurality of control droplets, each control droplet of the plurality of control droplets including copies of a respective control oligonucleotide of a plurality of control oligonucleotides, each control oligonucleotide of the plurality of control oligonucleotides having a known sequence and a corresponding identification: for each control droplet of the plurality of control droplets of the control partition: receiving a control hybridization signal indicating a hybridization of a sequencing probe from a plurality of sequencing probes with copies of the respective control oligonucleotide in the control droplet; determining the ID of the control oligonucleotide in the control droplet; mapping the control hybridization signal to a multi-dimensional control data point in a dye space; and storing the multi-dimensional control data point associated with the ID of the control oligonucleotide; for each sequencing probe of the plurality of sequencing probes: receiving a sequencing probe bit vector based on the known sequences of the plurality of control oligonucleotides, wherein each bit in the sequencing probe bit vector represents a presence or absence of the sequencing probe in a corresponding control oligonucleotide of the plurality of control oligonucleotides; receiving a first target hybridization signal for a first target droplet of a first target partition including copies of the target nucleic acid; mapping the first target hybridization signal to a first multi-dimensional target data point in the dye space; selecting a region in the dye space that includes the first multi-dimensional target data point; generating a region vector for the region, wherein each value in the region vector represents a contribution of any multi-dimensional control data points that are within the region and that have the ID of the corresponding control oligonucleotide; and identifying a first sequencing probe as hybridizing to the target nucleic acid based on a match condition between the region vector and a first sequencing probe bit vector for the first sequencing probe. for each control partition of a plurality of control partitions, each control partition including a plurality of control droplets, each control droplet of the plurality of control droplets including copies of a respective control oligonucleotide of a plurality of control oligonucleotides, each control oligonucleotide of the plurality of control oligonucleotides having a known sequence and a corresponding identification: for each control droplet of the plurality of control droplets of the control partition: receiving a control hybridization signal indicating a hybridization of a sequencing probe from a plurality of sequencing probes with copies of the respective control oligonucleotide in the control droplet; determining the ID of the control oligonucleotide in the control droplet; mapping the control hybridization signal to a multi-dimensional control data point in a dye space; and storing the multi-dimensional control data point associated with the ID of the control oligonucleotide; for each sequencing probe of the plurality of sequencing probes: receiving a sequencing probe bit vector based on the known sequences of the plurality of control oligonucleotides, wherein each bit in the sequencing probe bit vector represents a presence or absence of the sequencing probe in a corresponding control oligonucleotide of the plurality of control oligonucleotides; receiving a first target hybridization signal for a first target droplet of a first target partition including copies of the target nucleic acid; mapping the first target hybridization signal to a first multi-dimensional target data point in the dye space; selecting a region in the dye space that includes the first multi-dimensional target data point; generating a region vector for the region, wherein each value in the region vector represents a contribution of any multi-dimensional control data points that are within the region and that have the ID of the corresponding control oligonucleotide; and identifying a first sequencing probe as hybridizing to the target nucleic acid based on a match condition between the region vector and a first sequencing probe bit vector for the first sequencing probe. receiving a sequencing probe bit vector based on the known sequences of the plurality of control oligonucleotides, wherein each bit in the sequencing probe bit vector represents a presence or absence of the sequencing probe in a corresponding control oligonucleotide of the plurality of control oligonucleotides; receiving a first target hybridization signal for a first target droplet of a first target partition including copies of the target nucleic acid; mapping the first target hybridization signal to a first multi-dimensional target data point in the dye space; selecting a region in the dye space that includes the first multi-dimensional target data point; generating a region vector for the region, wherein each value in the region vector represents a contribution of any multi-dimensional control data points that are within the region and that have the ID of the corresponding control oligonucleotide; and identifying a first sequencing probe as hybridizing to the target nucleic acid based on a match condition between the region vector and a first sequencing probe bit vector for the first sequencing probe.