FPGA acceleration of DNA sequence alignment: design analysis and optimization

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. In this work, we propose a runtime reconfigurable alignment pipeline that considers all information in sequencing data for the biologically accurate acceleration of short read mapping. We focus our efforts on accelerating two string matching techniques: FM-index and the Smith-Waterman algorithm with the affine-gap model which are commonly used in short read mapping. We further optimize the FPGA hardware using a design analyzer and merger to improve alignment performance. The contributions of this work are as follows. 1. We accelerate the exact-match and mismatch alignment by leveraging the FM-index technique. We optimize memory access by compressing the data structure and interleaving the access with multiple short reads. The FM-index hardware also considers complete information in the read data to maximize accuracy. 2. We propose a seed-and-extend model to accelerate alignment with indels. The FM-index hardware is extended to support the seeding stage while a Smith-Waterman implementation with the affine-gap model is developed on FPGA for the extension stage. This model can improve the efficiency of indel alignment with comparable accuracy versus state-of-the-art software. 3. We present an approach for merging multiple FPGA designs into a single hardware design, so that multiple place-and-route tasks can be replaced by a single task to speed up functional evaluation of designs. We first experiment with this approach to demonstrate its feasibility for different designs. Then we apply this approach to optimize one of the proposed FPGA aligners for better alignment performance.Open Acces

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists

Mapping DSP algorithms to a reconfigurable architecture Adaptive Wireless Networking (AWGN)

This report will discuss the Adaptive Wireless Networking project. The vision of the Adaptive Wireless Networking project will be given. The strategy of the project will be the implementation of multiple communication systems in dynamically reconfigurable heterogeneous hardware. An overview of a wireless LAN communication system, namely HiperLAN/2, and a Bluetooth communication system will be given. Possible implementations of these systems in a dynamically reconfigurable architecture are discussed. Suggestions for future activities in the Adaptive Wireless Networking project are also given

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics

BlueDBM: An Appliance for Big Data Analytics

Complex data queries, because of their need for random accesses, have proven to be slow unless all the data can be accommodated in DRAM. There are many domains, such as genomics, geological data and daily twitter feeds where the datasets of interest are 5TB to 20 TB. For such a dataset, one would need a cluster with 100 servers, each with 128GB to 256GBs of DRAM, to accommodate all the data in DRAM. On the other hand, such datasets could be stored easily in the flash memory of a rack-sized cluster. Flash storage has much better random access performance than hard disks, which makes it desirable for analytics workloads. In this paper we present BlueDBM, a new system architecture which has flash-based storage with in-store processing capability and a low-latency high-throughput inter-controller network. We show that BlueDBM outperforms a flash-based system without these features by a factor of 10 for some important applications. While the performance of a ram-cloud system falls sharply even if only 5%~10% of the references are to the secondary storage, this sharp performance degradation is not an issue in BlueDBM. BlueDBM presents an attractive point in the cost-performance trade-off for Big Data analytics.Quanta Computer (Firm)Samsung (Firm)Lincoln Laboratory (PO7000261350)Intel Corporatio

Large-Scale MIMO Detection for 3GPP LTE: Algorithms and FPGA Implementations

Large-scale (or massive) multiple-input multiple-output (MIMO) is expected to be one of the key technologies in next-generation multi-user cellular systems, based on the upcoming 3GPP LTE Release 12 standard, for example. In this work, we propose - to the best of our knowledge - the first VLSI design enabling high-throughput data detection in single-carrier frequency-division multiple access (SC-FDMA)-based large-scale MIMO systems. We propose a new approximate matrix inversion algorithm relying on a Neumann series expansion, which substantially reduces the complexity of linear data detection. We analyze the associated error, and we compare its performance and complexity to those of an exact linear detector. We present corresponding VLSI architectures, which perform exact and approximate soft-output detection for large-scale MIMO systems with various antenna/user configurations. Reference implementation results for a Xilinx Virtex-7 XC7VX980T FPGA show that our designs are able to achieve more than 600 Mb/s for a 128 antenna, 8 user 3GPP LTE-based large-scale MIMO system. We finally provide a performance/complexity trade-off comparison using the presented FPGA designs, which reveals that the detector circuit of choice is determined by the ratio between BS antennas and users, as well as the desired error-rate performance.Comment: To appear in the IEEE Journal of Selected Topics in Signal Processin

Baseband Transceiver Design of a High Definition Radio FM System Using Joint Theoretical Analysis and FPGA Implementation

Advances in wireless communications have enabled various technologies for wireless digital communication. In the field of digital radio broadcasting, several specifications have been proposed, such as Eureka-147 and digital radio mondiale (DRM). These systems require a new spectrum assignment, which incurs heavy cost due to the depletion of the available spectrum. Therefore, the in-band on-channel (IBOC) system has been developed to work in the same band with the conventional analog radio and to provide digital broadcasting services. This paper discusses the function and algorithm of the high definition (HD) radio frequency modulation (FM) digital radio broadcasting system. Content includes data format allocation, constellation mapping, orthogonal frequency division multiplexing (OFDM) modulation of the transmitter, timing synchronization, OFDM demodulation, integer and fraction carrier frequency (integer carrier frequency offset (ICFO) and fractional CFO (FCFO)) estimation, and channel estimation of the receiver. When we implement this system to the field programmable gate array (FPGA) based on a hardware platform, both theoretical and practical aspects have been considered to accommodate the available hardware resources