0000000000230285
AUTHOR
Yupeng Chen
showing 5 related works from this author
Accelerating short read mapping on an FPGA (abstract only)
2012
The explosive growth of short read datasets produced by high throughput DNA sequencing technologies poses a challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. Although a number of short read mapping software tools have been proposed, designs based on hardware are relatively rare. In this paper, we present a hybrid system for short read mapping utilizing both software and field programmable gate array (FPGA)-based hardware. The compute intensive semi-g…
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN
2013
BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the…
An FPGA aligner for short read mapping
2012
The rapid growth of short read datasets poses a new challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. In this work, we present a parallel architecture for short read mapping utilizing field programmable gate array (FPGA)-based hardware. The computation intensive semi-global alignment and the hash table lookup operations are mapped onto an FPGA. The proposed Align Core is implemented with a parallel block structure to gain computational efficiency. We present a new parallel block-wise alignment structure to approximate the conventional dynamic programming algorithm. The performance of our FPGA aligner is compared to the GASSST and BWA …
The enhanced X-ray Timing and Polarimetry mission—eXTP
2019
In this paper we present the enhanced X-ray Timing and Polarimetry mission - eXTP. eXTP is a space science mission designed to study fundamental physics under extreme conditions of density, gravity and magnetism. The mission aims at determining the equation of state of matter at supra-nuclear density, measuring effects of QED, and understanding the dynamics of matter in strong-field gravity. In addition to investigating fundamental physics, eXTP will be a very powerful observatory for astrophysics that will provide observations of unprecedented quality on a variety of galactic and extragalactic objects. In particular, its wide field monitoring capabilities will be highly instrumental to det…
A hybrid short read mapping accelerator
2013
Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a compet…