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MEGAN - Metagenome Analysis
Software
by Daniel Huson and Stephan
Schuster,
with contributions from Alexander F. Auch,
Daniel C. Richter, Suparna Mitra and
Qi Ji.
Metagenomics
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 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:
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.
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:
Simulated datasets used in the paper:
Internal.
Recent presentations
Methods for metagenomic analysis (U Penn, Penn State and Venter
Institute, April 2008)
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