Imperial College London


Faculty of EngineeringDepartment of Computing

Professor of Computer Engineering



+44 (0)20 7594 8313w.luk Website




434Huxley BuildingSouth Kensington Campus






BibTex format

author = {Arram, J and Pflanzer, M and Kaplan, T and Luk, W},
doi = {10.1109/FPT.2015.7393126},
publisher = {IEEE},
title = {FPGA acceleration of reference-based compression for genomic data},
url = {},
year = {2016}

RIS format (EndNote, RefMan)

AB - One of the key challenges facing genomics today is efficiently storing the massive amounts of data generated by next-generation sequencing platforms. Reference-based compression is a popular strategy for reducing the size of genomic data, whereby sequence information is encoded as a mapping to a known reference sequence. Determining the mapping is a computationally intensive problem, and is the bottleneck of most reference-based compression tools currently available. This paper presents the first FPGA acceleration of reference-based compression for genomic data. We develop a new mapping algorithm based on the FM-index search operation which includes optimisations targeting the compression ratio and speed. Our hardware design is implemented on a Maxeler MPC-X2000 node comprising 8 Altera Stratix V FPGAs. When evaluated against compression tools currently available, our tool achieves a superior compression ratio, compression time, and energy consumption for both FASTA and FASTQ formats. For example, our tool achieves a 30% higher compression ratio and is 71.9 times faster than the fastqz tool.
AU - Arram,J
AU - Pflanzer,M
AU - Kaplan,T
AU - Luk,W
DO - 10.1109/FPT.2015.7393126
PY - 2016///
TI - FPGA acceleration of reference-based compression for genomic data
UR -
UR -
ER -