Metaspark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes
文献类型：期刊论文
| 作者 | Zhou, Wei1; Li, Ruilin2,3; Yuan, Shuo1; Liu, ChangChun1; Yao, Shaowen1; Luo, Jing4,5; Niu, Beifang2,3 |
| 刊名 | Bioinformatics
 |
| 出版日期 | 2017-04-01 |
| 卷号 | 33期号:7页码:1090-1092 |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btw750 |
| 通讯作者 | Luo, jing(jingluo@ynu.edu.cn) ; Niu, beifang(bniu@sccas.cn) |
| 英文摘要 | A with the advent of next-generation sequencing, traditional bioinformatics tools are challenged by massive raw metagenomic datasets. one of the bottlenecks of metagenomic studies is lack of large-scale and cloud computing suitable data analysis tools. in this paper, we proposed a spark-based tool, called metaspark, to recruit metagenomic reads to reference genomes. metaspark benefits from the distributed data set (rdd) of spark, which makes it able to cache data set in memory across cluster nodes and scale well with the datasets. compared with previous metagenomics recruitment tools, metaspark recruited significantly more reads than many programs such as soap2, bwa and last and increased recruited reads by similar to 4% compared with frhit when there were 1 million reads and 0.75gb references. different test cases demonstrate metaspark's scalability and overall high performance. |
| WOS关键词 | ALIGNMENT ; PROGRAM ; SCALE |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| 语种 | 英语 |
| 出版者 | OXFORD UNIV PRESS |
| WOS记录号 | WOS:000400984700020 |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2374221 |
| 专题 | 计算机网络信息中心 |
| 通讯作者 | Luo, Jing; Niu, Beifang |
| 作者单位 | 1.Yunnan Univ, Sch Software, Kunming, Peoples R China 2.Chinese Acad Sci, Comp Network Informat Ctr, Beijing, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100190, Peoples R China 4.Yunnan Univ, Sch Life Sci, Kunming, Peoples R China 5.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresources Y, Kunming, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhou, Wei,Li, Ruilin,Yuan, Shuo,et al. Metaspark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes[J]. Bioinformatics,2017,33(7):1090-1092. |
| APA | Zhou, Wei.,Li, Ruilin.,Yuan, Shuo.,Liu, ChangChun.,Yao, Shaowen.,...&Niu, Beifang.(2017).Metaspark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes.Bioinformatics,33(7),1090-1092. |
| MLA | Zhou, Wei,et al."Metaspark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes".Bioinformatics 33.7(2017):1090-1092. |
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