SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

doi:10.1186/1471-2105-15-S9-S2

	SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
	Meng,Jintao 1,2,3; Wang,Bingqiang 4; Wei,Yanjie 1; Feng,Shengzhong 1; Balaji,Pavan 5
	2014-09-10
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	15 期号:Suppl 9
摘要	AbstractBackgroundThere is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data.ResultsThis paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets.ConclusionsIn this paper, we presented a highly scalable and efficient genome assembly software, SWAP-Assembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler
关键词	genome assembly parallel computing De Bruijn graph
DOI	10.1186/1471-2105-15-S9-S2
语种	英语
WOS记录号	BMC:10.1186/1471-2105-15-S9-S2
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4041
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Wei,Yanjie
作者单位	1.Chinese Academy of Sciences; Shenzhen Institutes of Advanced Technology 2.Chinese Academy of Sciences; Institute of Computing Technology 3.University of Chinese Academy of Sciences 4.Beijing Genomics Institute 5.Argonne National Laboratory; Mathematics and Computer Science Division
推荐引用方式 GB/T 7714	Meng,Jintao,Wang,Bingqiang,Wei,Yanjie,et al. SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores[J]. BMC Bioinformatics,2014,15(Suppl 9).
APA	Meng,Jintao,Wang,Bingqiang,Wei,Yanjie,Feng,Shengzhong,&Balaji,Pavan.(2014).SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.BMC Bioinformatics,15(Suppl 9).
MLA	Meng,Jintao,et al."SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores".BMC Bioinformatics 15.Suppl 9(2014).