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Lloyd et al. were first to demonstrate the promise of quantum algorithms for computing Betti numbers, a way to characterize topological features of data sets. Here, we propose, analyze, and optimize an improved quantum algorithm for topological data analysis (TDA) with reduced scaling, including a method for preparing Dicke states based on inequality testing, a more efficient amplitude estimation algorithm using Kaiser windows, and an optimal implementation of eigenvalue projectors based on Chebyshev polynomials. We compile our approach to a fault-tolerant gate set and estimate constant factors in the Toffoli complexity. Our analysis reveals that super-quadratic quantum speedups are only possible for this problem when targeting a multiplicative error approximation and the Betti number grows asymptotically. Further, we propose a dequantization of the quantum TDA algorithm that shows that having exponentially large dimension and Betti number are necessary, but insufficient conditions, for super-polynomial advantage. We then introduce and analyze specific problem examples which have parameters in the regime where super-polynomial advantages may be achieved, and argue that quantum circuits with tens of billions of Toffoli gates can solve seemingly classically intractable instances.