This paper studies the estimation of a large covariance matrix. We introduce a novel procedure called ChoSelect based on the Cholesky factor of the inverse covariance. This method uses a dimension reduction strategy by selecting the pattern of zero of the Cholesky factor. Alternatively, ChoSelect can be interpreted as a graph estimation procedure for directed Gaussian graphical models. Our approach is particularly relevant when the variables under study have a natural ordering (e.g. time series) or more generally when the Cholesky factor is approximately sparse. ChoSelect achieves non-asymptotic oracle inequalities with respect to the Kullback-Leibler entropy. Moreover, it satisfies various adaptive properties from a minimax point of view. We also introduce and study a two-stage procedure that combines ChoSelect with the Lasso. This last method enables the practitioner to choose his own trade-off between statistical efficiency and computational complexity. Moreover, it is consistent under weaker assumptions than the Lasso. The practical performances of the different procedures are assessed on numerical examples.