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
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http://soils.usda.gov	Venter et al. 2004	Poinar et al 2006

The taxonomical content of such a sample is usually estimated by comparison against DNA and protein sequence databases of known sequences. Most published studies employ the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging very-high-throughput sequencing technologies are paving the way to low-cost random shotgun approaches.

Laptop Analysis

MEGAN (“MEtaGenome ANalyzer”) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.

Assignment of Reads to Taxa

An LCA-based algorithm assigns reads to taxa in such a way that the taxonomical level of the assigned taxon reflects the level of conservation of the sampled sequence. The software allows dissection of large datasets without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for the comparison of different data sets. We have sucessfully applied this approach to a number of datasets obtained by Sanger sequencing and sequencing-by-synthesis technology, including the Sargasso Sea dataset, a recently published metagenomic dataset sampled from a mammoth bone, and several complete microbial genomes.

Comparison and Analysis of Multiple Datasets

We are working on a new version of the program, called MEGAN2, that is aimed at facilitiating comparative analyses of datasets.
As a simple example, this pictures shows the analysis of two different sequencing experiments performed on Ecoli and on Bdellovibrio,
using 454 sequencing. It clearly illustrates that MEGAN analysis can distinguish between the two different species, based on a BlastX comparison against NR:

simple comparison between two different datasets

simple comparison between two different datasets

COG analysis

MEGAN2 provides tools for analysing the functional content of a metagenome:

Publications

An example of the application of MEGAN can be found in Poinar et al 2006., where we used an early version of our software (called GenomeTaxonomyBrowser) to analyze the taxonomical content of a collection of DNA reads sampled from a mammoth.

See the online advanced publication of our paper entitled "MEGAN Analysis of Metagenomic Data" in Genome Research.

Download

Use of the program requires a license. Academic licenses are freely available to all academic users. Usage in non-academic settings requires a commerical license. Obtain a license key online.

We are currently developing MEGAN2, a new comparative version of MEGAN. Download the latest BETA version here.

(Download the original version 1.0 here.)

To find out more about the program, please take a look at the current user manual.

Screen casts

Introduction to MEGAN2beta:

Advanced features of MEGAN2beta:

coming soon...

Comparative analysis using MEGAN2beta:

coming soon...

Datasets

Here are links to data sets used in our paper "MEGAN Analysis of Metagenome Data" which appeared in Genome Research:

Sargasso Sea Subsample 1	10,000 Sanger reads	BLASTX-NR	MEGAN file
Sargasso Sea Subsample 2-4	10,000 Sanger reads	BLASTX-NR	MEGAN file
Mammoth dataset		BLASTX-NR	MEGAN file
E. coli K12	2000 SBS reads	BLASTX-NR	MEGAN file MEGAN file without K12 hits
Bdellovibrio bacteriovorus HD100	2000 SBS reads	BLASTX-NR	MEGAN file MEGAN file without HD100 hits

Simulated datasets used in the paper:

E. coli K12, simulated reads ~35 bp	5000 SBS reads	MEGAN file
E. coli K12, simulated reads ~100 bp	5000 SBS reads	MEGAN file
E. coli K12, simulated reads ~200 bp	5000 SBS reads	MEGAN file
E. coli K12, simulated reads ~800 bp	5000 SBS reads	MEGAN file
B. bacteriovorus HD100, simulated reads ~35 bp	5000 SBS reads	MEGAN file
B. bacteriovorus HD100, simulated reads ~100 bp	5000 SBS reads	MEGAN file
B. bacteriovorus HD100, simulated reads ~200 bp	5000 SBS reads	MEGAN file
B. bacteriovorus HD100, simulated reads ~800 bp	5000 SBS reads	MEGAN file

Internal.

Recent presentations

Methods for metagenomic analysis (U Penn, Penn State and Venter Institute, April 2008)