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Barcode Collision Calculator

In combinatorial indexing experiments, each cell is assigned a barcode by sampling from a pool of possible combinations. When two or more cells receive the same barcode, a collision occurs — analogous to the classic birthday problem in probability theory.

This calculator estimates the expected fraction of cells involved in barcode collisions given your experimental parameters.

Number of unique barcodes per round.
Number of rounds of combinatorial indexing.
Number of barcoded cells sampled for sequencing.
Collision Rate
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Barcode Pool Size
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Expected Collisions
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Collision Rate vs. Number of Cells
How it works
For each cell, the probability that no other cell shares its barcode is:
P(unique) = ((k - 1) / k) ^ (n - 1)

where k = total barcode combinations and n = number of cells.

The expected collision rate (fraction of cells sharing a barcode) is:
collision rate = 1 - ((k - 1) / k) ^ (n - 1)

For large k, this approximates to: 1 - e^(-(n-1)/k)

This is equivalent to the simulation: sampling n barcodes uniformly from k options with replacement, then counting the fraction assigned to non-unique barcodes.