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The recently conjectured knots-quivers correspondence (Kucharski et al. in Phys Rev D 96(12):121902, 2017. arXiv:1707.02991, Adv Theor Math Phys 23(7):1849–1902, 2019. arXiv:1707.04017) relates gauge theoretic invariants of a knot K in the 3-sphere to the representation theory of a quiver Q K associated to the knot. In this paper we provide geometric and physical contexts for this conjecture within the framework of Ooguri-Vafa large N duality (Ooguri and Vafa in Nucl Phys B 577:419–438, 2000), that relates knot invariants to counts of holomorphic curves with boundary on L K , the conormal Lagrangian of the knot in the resolved conifold, and corresponding M-theory considerations. From the physics side, we show that the quiver encodes a 3d N = 2 theory T [ Q K ] whose low energy dynamics arises on the worldvolume of an M5 brane wrapping the knot conormal and we match the (K-theoretic) vortex partition function of this theory with the motivic generating series of Q K . From the geometry side, we argue that the spectrum of (generalized) holomorphic curves on L K is generated by a finite set of basic disks. These disks correspond to the nodes of the quiver Q K and the linking of their boundaries to the quiver arrows. We extend this basic dictionary further and propose a detailed map between quiver data and topological and geometric properties of the basic disks that again leads to matching partition functions. We also study generalizations of A-polynomials associated to Q K and (doubly) refined version of LMOV invariants (Ooguri and Vafa 2000; Labastida and Marino in Commun Math Phys 217(2):423–449, 2001. arXiv:hep-th/0004196; Labastida et al. in JHEP 11:007, 2000. arXiv:hep-th/0010102; Aganagic and Vafa in Large N duality, mirror symmetry, and a Q-deformed A-polynomial for knots. arXiv:1204.4709; Fuji et al. in Nucl Phys B 867:506–546, 2013. arXiv:1205.1515). [ABSTRACT FROM AUTHOR]