FAssem : FPGA based Acceleration of De Novo Genome Assembly

Sharat Chandra Varma (1) , Paul Kolin (1) , M. Balakrishnan (1) , Dominique Lavenier (2)

1 Department of Computer Science and Engineering [New Delhi]
2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics

Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

Mots clés: FPGA; Acceleration; Next Generation Sequencing Assembly; Bioinformatics

Domaines: Architectures Matérielles [cs.AR]; Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Sharat Chandra Varma, Paul Kolin, M. Balakrishnan, Dominique Lavenier. FAssem : FPGA based Acceleration of De Novo Genome Assembly. Proceeding of The 21st Annual International IEEE Symposium on Field Programmable Custom Computing Machines, Apr 2013, Seattle, United States. pp.FCCM'2013. ⟨hal-00829055⟩