BarraCUDA - a fast short read sequence aligner using graphics processing units

Klus, Petr; Lam, Simon; Lyberg, Dag; Cheung, Ming Sin; Pullan, Graham; McFarlane, Ian G.; Yeo, Giles S.H.; Lam, Brian

doi:10.1186/1756-0500-5-27

Cited by 123 publications

(87 citation statements)

References 23 publications

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“…BarraCUDA r280 [28] is evaluated for GPU platform of FM-index case, which is the accelerated version of BWA. The short read dataset and reference genome are the same as hash-index based tests.…”

Section: Test Resultsmentioning

confidence: 99%

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3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

Liu

Hemani

Paul

et al. 2017

Int J Parallel Prog

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Sequence analysis plays extremely important role in bioinformatics, and most applications of which have compute intensive kernels consuming over 70% of total execution time. By exploiting the compute intensive execution stages of popular sequence analysis applications, we present and evaluate a VLSI architecture with a focus on those that target at biological sequences directly, including pairwise sequence alignment, multiple sequence alignment, database search, and short read sequence mappings. Based on coarse grained reconfigurable array we propose the use of many-core and 3D-stacked technologies to gain further improvement over memory subsystem, which gives another order of magnitude speedup from high bandwidth and low access latency. We analyze our approach in terms of its throughput and efficiency for different application mappings. Initial experimental results are evaluated from a stripped down implementation in a commodity FPGA, and then we scale the results to estimate the performance of our architecture with 9 layers of 70 mm 2 stacked wafers in 45-nm process. We demonstrate numerous estimated speedups better than corresponding existed hardware accelerator platforms for at least 40 times for the entire range of applications and datasets of interest. In comparison, the alternative FPGA based accelerators deliver only improvement for single application, while GPGPUs perform not well enough on accelerating program kernel with random memory access and integer addition/comparison operations.

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Section: Test Resultsmentioning

confidence: 99%

“…A great number of papers have been published that either use FPGAs [16][17][18][19][20][21]55], or GPUs [28][29][30].…”

Section: Related Workmentioning

confidence: 99%

3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

Liu

Hemani

Paul

et al. 2017

Int J Parallel Prog

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“…Bisulfite sequencing alignment is computationally intensive and can take days and weeks of processing time. Some new approaches seek to utilize computer hardware differently to greatly speed bisulfite sequencing alignments (Klus et al 2012;Koster and Rahmann 2014;Manconi et al 2014). With quality controlled and aligned sequencing data, quantitation of methylation levels is the next stage of analysis.…”

Section: Bioinformaticsmentioning

confidence: 99%

Analysis of DNA modifications in aging research

et al. 2018

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As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through nextgeneration sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-theart for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.

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“…However, increasing the speed of alignment process provides time saving, especially with regard to processing large-scale data; hence, a multiple-core Graphics Processing Units (GPUs)-based method is a powerful choice. There are several alignment tools based on GPU, including SOAP3 [17] and BarraCUDA [18].…”

Section: Introductionmentioning

confidence: 99%

BWTaligner: a genome short-read aligner

Nguyen¹,

Trinh²,

Trinh³

et al. 2018

VJSTE

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Abstract:The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads -small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression -exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA -the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth.

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BarraCUDA - a fast short read sequence aligner using graphics processing units

Cited by 123 publications

References 23 publications

3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

Analysis of DNA modifications in aging research

BWTaligner: a genome short-read aligner

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