The high throughput of modern NGS sequencers coupled with the huge sizes of genomes currently analysed, poses always higher algorithmic challenges to align short reads quickly and accurately against a reference sequence. A crucial, additional, requirement is that the data structures used should be light. The available modern solutions usually are a compromise between the mentioned constraints: in particular, indexes based on the Burrows-Wheeler transform offer reduced memory requirements at the price of lower sensitivity, while hash-based text indexes guarantee high sensitivity at the price of significant memory consumption.