Computational Challenges of Next Generation Sequencing Pipelines Using Heterogeneous Systems

Computational Challenges of Next Generation Sequencing Pipelines Using Heterogeneous Systems

Houtgast, E.J. (TU Delft Computer Engineering; Bluebee, Rijswijk)
Sima, V.M. (Bluebee, Rijswijk)
Bertels, K.L.M. (TU Delft Quantum & Computer Engineering; TU Delft FTQC/Bertels Lab)
Al-Ars, Z. (TU Delft Computer Engineering)

Quantum & Computer Engineering

2016

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.

BWA-MEM
FPGA
GPU
Next Generation Sequencing

http://resolver.tudelft.nl/uuid:217651c0-007b-4b40-8c2d-c53cbf1549fd

1-4

12th International Summer School on Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems, 2016-07-10 → 2016-07-16, Fiuggi, Italy

Institutional Repository

abstract

© 2016 E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars