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The notion of Gem-Matveev complexity has been introduced within crystallization theory, as a combinatorial method to estimate Matveev’s complexity of closed 3-manifolds; it yielded upper bounds for interesting classes of such manifolds. In this paper we extend the definition to the case of non-empty boundary and prove that for each compact irreducible and boundary-irreducible 3-manifold it coincides with the modified Heegaard complexity introduced by Cattabriga, Mulazzani and Vesnin. Moreover, via Gem-Matveev complexity, we obtain an estimation of Matveev’s complexity for all Seifert 3-manifolds with base and two exceptional fibers and, therefore, for all torus knot complements.

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