Question answering (QA) systems often consist of several components such as Named Entity Disambiguation (NED), Relation Extraction (RE), and Query Generation (QG). In this paper, we focus on the QG process of a QA pipeline on a large-scale Knowledge Base (KB), with noisy annotations and complex sentence structures. We therefore propose SQG, a SPARQL Query Generator with modular architecture, enabling easy integration with other components for the construction of a fully functional QA pipeline. SQG can be used on large open-domain KBs and handle noisy inputs by discovering a minimal subgraph based on uncertain inputs, that it receives from the NED and RE components. This ability allows SQG to consider a set of candidate entities/relations, as opposed to the most probable ones, which leads to a significant boost in the performance of the QG component. The captured subgraph covers multiple candidate walks, which correspond to SPARQL queries. To enhance the accuracy, we present a ranking model based on Tree-LSTM that takes into account the syntactical structure of the question and the tree representation of the candidate queries to find the one representing the correct intention behind the question