CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing
文献类型：期刊论文
| 作者 | Zhao Guoguang1; Bu Dechao1; Liu Changning1; Li Jing1; Yang Jian3; Liu Zhiyong1; Zhao Yi1; Chen Runsheng1 |
| 刊名 | PROTEIN & CELL
 |
| 出版日期 | 2012 |
| 卷号 | 3期号:2页码:148 |
| 关键词 | CloudLCA metagenome analysis cloud computing |
| ISSN号 | 1674-800X |
| 英文摘要 | Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis. However, extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software. Here, we present CloudLCA, a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis. Results show that CloudLCA (1) has a running time nearly linear with the increase of dataset magnitude, (2) displays linear speedup as the number of processors grows, especially for large datasets, and (3) reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes. In comparison with MEGAN, a well-known metagenome analyzer, the speed of CloudLCA is up to 5 more times faster, and its peak memory usage is approximately 18.5% that of MEGAN, running on a fat node. CloudLCA can be run on one multiprocessor node or a cluster. It is expected to be part of MEGAN to accelerate analyzing reads, with the same output generated as MEGAN, which can be import into MEGAN in a direct way to finish the following analysis. Moreover, CloudLCA is a universal solution for finding the lowest common ancestor, and it can be applied in other fields requiring an LCA algorithm. |
| 语种 | 英语 |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/33287]  |
| 专题 | 中国科学院计算技术研究所期刊论文_中文 |
| 作者单位 | 1.中国科学院计算技术研究所 2.中国科学院大学 3.Chinese Ctr Dis Control & Prevent, Natl Institute Viral Dis Control & Prevent, State Key Lab Mol Virol & Genet Engn, Beijing 100176, Peoples R China Natl Institute Viral Dis Control & Prevent State Key Lab Mol Virol & Genet Engn 4.Chinese Acad Science, Bioinformat Lab, Beijing 100101, Peoples R China Bioinformat Lab 5.中国科学院 |
| 推荐引用方式 GB/T 7714 | Zhao Guoguang,Bu Dechao,Liu Changning,et al. CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing[J]. PROTEIN & CELL,2012,3(2):148. |
| APA | Zhao Guoguang.,Bu Dechao.,Liu Changning.,Li Jing.,Yang Jian.,...&Chen Runsheng.(2012).CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing.PROTEIN & CELL,3(2),148. |
| MLA | Zhao Guoguang,et al."CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing".PROTEIN & CELL 3.2(2012):148. |
入库方式： OAI收割
来源：计算技术研究所
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