title: CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing.
abstract: 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.
authors.affiliation: Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Guoguang
authors.initials: G
authors.lastname: Zhao
authors.forename: Dechao
authors.initials: D
authors.lastname: Bu
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Liu
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D056186:Metagenomics; D057386:Search Engine; D014584:User-Computer Interface