We provide a physical definition of new homological invariants $mathcal{H}_a (M_3)$ of 3-manifolds (possibly, with knots) labeled by abelian flat connections. The physical system in question involves a 6d fivebrane theory on $M_3$ times a 2-disk, $D^2$, whose Hilbert space of BPS states plays the role of a basic building block in categorification of various partition functions of 3d $mathcal{N}=2$ theory $T[M_3]$: $D^2times S^1$ half-index, $S^2times S^1$ superconformal index, and $S^2times S^1$ topologically twisted index. The first partition function is labeled by a choice of boundary condition and provides a refinement of Chern-Simons (WRT) invariant. A linear combination of them in the unrefined limit gives the analytically continued WRT invariant of $M_3$. The last two can be factorized into the product of half-indices. We show how this works explicitly for many examples, including Lens spaces, circle fibrations over Riemann surfaces, and plumbed 3-manifolds.
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