MEGAN analysis of metagenomic data. Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random “shotgun” approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented

References in zbMATH (referenced in 17 articles )

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  1. Shah, Nidhi; Altschul, Stephen F.; Pop, Mihai: Outlier detection in BLAST hits (2017)
  2. Shi, Pixu; Zhang, Anru; Li, Hongzhe: Regression analysis for microbiome compositional data (2016)
  3. Jiang, Xingpeng; Weitz, Joshua S.; Dushoff, Jonathan: A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data (2012)
  4. Garbarine, Elaine; DePasquale, Joseph; Gadia, Vinay; Polikar, Robi; Rosen, Gail: Information-theoretic approaches to SVM feature selection for metagenome read classification (2011)
  5. Nalbantoglu, Ozkan U.; Way, Samuel F.; Hinrichs, Steven H.; Sayood, Khalid: Raiphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles (2011) ioport
  6. Fischer, Johannes; Huson, Daniel H.: New common ancestor problems in trees and directed acyclic graphs (2010)
  7. Mitra, Suparna; Schubach, Max; Huson, Daniel H.: Short clones or long clones? A simulation study on the use of paired reads in metagenomics (2010) ioport
  8. Yang, Bin; Peng, Yu; Leung, Henry Chi-Ming; Yiu, Siu-Ming; Chen, Jing-Chi; Chin, Francis Yuk-Lun: Unsupervised binning of environmental genomic fragments based on an error robust selection of (l)-mers (2010) ioport
  9. Diaz, Naryttza N.; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W.: TACOA - taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach (2009) ioport
  10. Gerlach, Wolfgang; Jünemann, Sebastian; Tille, Felix; Goesmann, Alexander; Stoye, Jens: Webcarma: a web application for the functional and taxonomic classification of unassembled metagenomic reads (2009) ioport
  11. Huson, Daniel H.; Richter, Daniel C.; Mitra, Suparna; Auch, Alexander F.; Schuster, Stephan C.: Methods for comparative metagenomics (2009) ioport
  12. Kislyuk, Andrey; Bhatnagar, Srijak; Dushoff, Jonathan; Weitz, Joshua S.: Unsupervised statistical clustering of environmental shotgun sequences (2009) ioport
  13. Li, Weizhong: Analysis and comparison of very large metagenomes with fast clustering and functional annotation (2009) ioport
  14. Wooley, John C.; Ye, Yuzhen: Metagenomics: facts and artifacts, and computational challenges (2009) ioport
  15. Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad: Metagenome fragment classification using (N)-mer frequency profiles (2008) ioport
  16. Schloss, Patrick; Handelsman, Jo: A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities (2008) ioport
  17. Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula: Dendroscope: An interactive viewer for large phylogenetic trees (2007) ioport