The advent of high-throughput sequencing platforms brought bioinformatics to a new level. This, so called ‘next-generation’ sequencing technology opened the researching doors of every laboratory allowing accomplishment of previously unimaginable scale and expensive experiments. As a result, novel research areas have emerged providing huge amounts of new data ready to be analyzed. Parallel to this progress, a variety of sequencing tools designed for data analysis has been published. Sequence alignment takes the central challenge in data analysis, providing primary representative results for the experiments. Few alignment methods and diversity of tools have been published and developed in the last years. The main goal of all these alignment tools is to fit between performance and accuracy. In this review will be presented the new NGS technologies and platforms, the current alignment approaches applied in data analysis and described some commonly used implementations of the methods.
next-generation sequencing, alignment algorithm, short reads