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The decline in abundance of Lyman-$\alpha$ (Ly$\alpha$) emitting galaxies at$z \gtrsim 6$ is a powerful and commonly used probe to constrain the progressof cosmic reionization. We use the CoDaII simulation, which is a radiationhydrodynamic simulation featuring a box of $\sim 94$ comoving Mpc side length,to compute the Ly$\alpha$ transmission properties of the intergalactic medium(IGM) at $z\sim 5.8$ to $7$. Our results mainly confirm previous studies, i.e.,we find a declining Ly$\alpha$ transmission with redshift and a largesightline-to-sightline variation. However, motivated by the recent discovery ofblue Ly$\alpha$ peaks at high redshift, we also analyze the IGM transmission onthe blue side, which shows a rapid decline at $z\gtrsim 6$ of the bluetransmission. This low transmission can be attributed not only to the presenceof neutral regions but also to the residual neutral hydrogen within ionizedregions, for which a density even as low as $n_{\rm HI}\sim10^{-9}\,\mathrm{cm}^{-3}$ (sometimes combined with kinematic effects) leads toa significantly reduced visibility. Still, we find that $\sim 1\%$ ofsightlines towards $M_{\mathrm{1600AB}}\sim -21$ galaxies at $z\sim 7$ aretransparent enough to allow a transmission of a blue Ly$\alpha$ peak. Wediscuss our results in the context of the interpretation of observations.

Lyman-alpha transmission properties of the intergalactic medium in the CoDaII simulation