An FPGA-Based Computing Infrastructure Tailored to Efficiently Scaffold Genome Sequences

In the current years broad access to genomic data is leading to improve the understanding and prevention of human diseases as never before. De-novo genome assembly, represents a main obstacle to perform the analysis on a large scale, as it is one of the most time-consuming phases of the genome analy...

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Bibliographic Details
Main Authors: Zeni, Alberto, Crespi, Matteo, Di Tucci, Lorenzo, Santambrogio, Marco D.
Format: Conference Proceeding
Language:English
Subjects:
Bioinformatics
Computer architecture
exact matching
Field programmable gate arrays
FPGA
genome assembly
Genomics
scaffolding
Software
Software algorithms
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Summary:In the current years broad access to genomic data is leading to improve the understanding and prevention of human diseases as never before. De-novo genome assembly, represents a main obstacle to perform the analysis on a large scale, as it is one of the most time-consuming phases of the genome analysis. In this paper, we present a scalable, high performance and energy efficient architecture for the alignment step of SSPACE, a state of the art tool used to perform scaffolding also in case of de-novo assembly. The final architecture is able to achieve up to 9.83x speedup in performance when compared to the software version of Bowtie, a state of the art tool used by SSPACE to perform the alignment.
ISSN:2576-2621
DOI:10.1109/FCCM.2019.00074