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We show that the supersymmetric partition function of three-dimensional N=2 R-symmetric Chern-Simons-matter theories on the squashed S^3 and on S^2 x S^1 can be computed with the so-called Higgs branch localization method, alternative to the more standard Coulomb branch localization. For theories that could be completely Higgsed by Fayet-Iliopoulos terms, the path integral is dominated by BPS vortex strings sitting at two circles in the geometry. In this way, the partition function directly takes the form of a sum, over a finite number of points on the classical Coulomb branch, of a vortex-string times an antivortex-string partition functions.

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