Census-based rapid and accurate metagenome taxonomic profiling

BMC Genomics

Raja Mazumder⁵  Amy Zanne⁷  Vahan Simonyan¹  Mariya Shcheglovitova²  Konstantinos Krampis³  W Evan Johnson⁴  Yang Pan⁶  Amirhossein Shamsaddini⁶ 

[1] Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville 20852, MD, USA;Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA;Bioinformatics Department, The J. Craig Venter Institute, Rockville, MD 20850, USA;Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA;McCormick Genomic and Proteomic Center, George Washington University, Washington DC 20037, USA;Department of Biochemistry and Molecular Medicine, George Washington University, Washington DC 20037, USA;Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO 63166, USA

关键词: Diagnostics;    Taxonomic profiling;    Next-gen sequence analysis;    Census-based;    Metagenome;   

Others  :  1128438
DOI  :  10.1186/1471-2164-15-918

 received in 2013-09-11, accepted in 2014-10-06,  发布年份 2014

【 摘 要 】

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.

Conclusion

CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope webcite. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.

【 授权许可】

   
2014 Shamsaddini et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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