We are rapidly entering the era of genomics. The dramatic cost reduction of DNA sequencing due to the introduction of Next Generation Sequencing (NGS) techniques has resulted in an exponential growth of genetics data. The amount of data generated, and its associated processing into useful information, poses serious computational challenges. Here, we give a brief introduction of NGS, show a typical NGS processing pipeline, and show the associated challenges from a computational perspective. A case study is presented where one component of the NGS processing pipeline is accelerated: BWA-MEM, the de-facto industry-standard for the mapping stage. This is a first step in achieving a fully heterogeneously accelerated NGS pipeline.
|Number of pages||4|
|Publication status||Published - 2016|
|Event||12th International Summer School on Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems - Fiuggi, Italy|
Duration: 10 Jul 2016 → 16 Jul 2016
|Other||12th International Summer School on Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems|
|Abbreviated title||ACACES 2016|
|Period||10/07/16 → 16/07/16|
- Next Generation Sequencing
Houtgast, E., Sima, V., Bertels, K., & Al-Ars, Z. (2016). Computational Challenges of Next Generation Sequencing Pipelines Using Heterogeneous Systems. 1-4. Abstract from 12th International Summer School on Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems, Fiuggi, Italy.