Pipelined multi-FPGA genomic data clustering

Wertenbroek, Rick (School of Management and Engineering Vaud, HES-SO // University of Applied Sciences Western Switzerland) ; Petraglio, Enrico (School of Management and Engineering Vaud, HES-SO // University of Applied Sciences Western Switzerland) ; Thoma, Yann (School of Management and Engineering Vaud, HES-SO // University of Applied Sciences Western Switzerland)

High throughput DNA sequencing made individual genome profiling possible and produces very large amounts of data. Today data and associated metadata are stored in FASTQ text file assemblies carrying the information of genome fragments called reads. Current techniques rely on mapping these reads to a common reference genome for compression and analysis. However, about 10% of the reads do not map to any known reference making them difficult to compress or process. These reads are of high importance because they hold information absent from any reference. Finding overlaps in these reads can help subsequent processing and compression tasks tremendously. Within this context clustering is used to find overlapping unmapped reads and sort them in groups. Clustering being an extremely time consuming task a modular multi-FPGA pipeline was designed and is the focus of this paper. A pipeline with 6 FPGAs was created and has shown a speed-up of ×5 compared to existing FPGA implementations. Resulting enriched files encoding reads and clustering results show file sizes within a 10% margin of the best DNA compressors while providing valuable extra information.


Keywords:
Conference Type:
full paper
Faculty:
Ingénierie et Architecture
School:
HEIG-VD
Institute:
ReDS - Reconfigurable & embedded Digital Systems
Subject(s):
Ingénierie
Publisher:
Helsinki, Finland, 21-23 August 2017
Date:
2017-08
Helsinki, Finland
21-23 August 2017
Pagination:
11 p.
Published in:
Lecture Notes in Computer Science ; Proceedings of 17th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2017, 21-23 August 2017, Helsinki, Finland
DOI:
ISSN:
0302-9743
ISBN:
978-3-319-65481-2
External resources:
Appears in Collection:

Note: The status of this file is: restricted


 Record created 2019-04-23, last modified 2019-04-23

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