Our work has addressed several issues relating to Ensemble Kalman Filter (EnKF) for assimilating real data, 1) model errors, 2) inconvenience or infeasibility of manually tuning the inflation factor when it is regional and/or variable dependent and 3) erroneously specified observation error statistics. A Local Ensemble Transform Kalman Filter (LETKF) is used as an efficient representative of other EnKF systems. For the model errors issue, we assimilate observations generated from the NCEP/NCAR reanalysis fields into the SPEEDY model. Several methods to handle model errors including model bias...