The advent of Next-Generation Sequencing (NGS) machines these past few years has enabled DNA sequencing to be done at a fraction of the cost and time of previous methods. However, compared to the handful of reads--thousand of bases in length--produced by traditional Sanger sequencing, NGS technologies produce billions of short reads only a few dozen bases in length. To cope with the massive influx of data, there has been a rush to develop new algorithms and software specialized for handling short reads that can efficiently keep up with the growing number and size of NGS operations around the world.

In this talk, we will survey various existing short read aligners, which locate the position of reads within a larger reference genome. Taking note of various design decisions and algorithms, we will then analyze the development of a NGS Alignment tool suite, which hopes to integrate, adapt and improve previously existing algorithms. Addressing the strengths and weaknesses of existing aligners, we aim not to create a single superior program, but a user-friendly open-source NGSA library, which will allow users to customize and build fundamentally different aligners tailored for the specific task on hand.