The absorption features in the spectra of distant quasar by intergalactic neutral hydrogen is one of the most sensitive observations that put strong constraints on the end stages of reionization. The main challenge lies in observing the high redshift quasar and modeling the patchy reionization in cosmological simulations. In this talk, we present the measurement of the photo-ionization rate ($\Gamma_{\rm HI}$),  the mean free path ($\lambda_{\rm mfp,HI}$) and the neutral fraction ($f_{\rm HI}$)  of hydrogen at redshift $4.85<z<6.05$ from a large sample of unprecedented quality quasar absorption spectra observed using XShooter (VLT) and ESI (Keck) instruments. The fluctuations in the ionizing radiation field are modeled by post-processing simulations from the Sherwood suite using our new code ``Extended reionization based on Code for Ionization and Temperature Evolution'' (Ex-CITE).  

Our measurements suggest that the hydrogen reionization is completed by $z \sim 5.3$. Our simulations show that the neutral islands persist down to $z \sim 5.3$ giving rise to long dark troughs seen in the observed spectra. Our simulation that matches the effective optical depth distribution also reproduces other statistics of the the Ly$\alpha$ forest at $z>5$ suggesting the robustness and accuracy of the measured parameters. Finally, we will discuss the implication of these measurements to our current cycle-2 JWST proposal and to future E-ELT / TMT observations.