Recent developments in next-generation sequencing technologies allow constantly increasing throughput and shorter running times while reducing the costs of the sequencing process. This leads to the production of huge amounts of data which raise important computation challenges not only due to the large volume of information but also to the increase of the reads length and sequencing errors. Several assembly and mapping tools have recently been developed for generating assemblies from short, unpaired sequencing reads. However, the need for faster and more accurate algorithmic approaches to keep up with the demand of frequently emerging resequencing projects, justify the growing number of short read mapping tools that surfaced in the last couple of years. In this report we present an overview of the state of the art software applications detailing their algorithms and data structures.