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MEGAN tutorial Friday July 30th, 2010

Material for workshop on metagenome analysis

Workshop - Friday July 30th, 2010 (website)

Location: University of Edinburgh, Pollock Hall Campus

Room: South Hall (

1:00 – 3:30 MEGAN - Metagenome Analysis Software - Daniel Huson



MEGAN is a program for analyzing random shotgun reads obtained by sequencing the DNA or RNA of a metagenome sample. It can also be used for denovo sequenced peptides (metaproteomics). The program assumes that you have performed a BLASTX comparison of your dataset against the NCBI-NR database.

To start working with MEGAN, you first use the File->Parse BLAST menu item to process your reads and BLAST file. When this set has been completed, you can then proceed to interactively analyze your dataset. Each dataset is stored in a so-called RMA file that contains all the reads and most of the BLAST matches (but uses only 30% of the space required by the original files). After opening multiple datasets, you can perform a comparative analysis using the File->Comparison menu item. For a functional analysis, open the SEED Viewer from the Window menu.

Talk download

Here is the current (but not final) version of the introductory talk that I will give:



Software download

The tutorial will use an alpha version of version 4 of MEGAN, available here:



Here is the current user manual for the program:


(The current released version of MEGAN is 3.9. We are currently working on a new release, version 4,  which will be available in November 2010. In the tutorial we will be using an "alpha" version MEGAN 4.0, because version 4.0 has a number of new features that are not available in 3.9. "Alpha" versions of software are usually only used for internal testing, but 4.0alpha8 is sufficiently stable for purposes of the tutorial. The user manual does not yet fully describe all new features of version 4 the program.)

License key

Use of the program requires that you obtain and enter a license key. This is free of charge for academic users and can be obtained here.

Datasets download

NEW: Please try to download the following file during the talk, as it contains a SOIL metagenome and thus has more fungal sequences than the gut samples below:


(This file is 1GB and will take at least 20 minutes to download)

The tutorial will use the following mouse gut datasets:






Here is a MEGAN comparison file for the above files:


Raw data download

The above files are (MEGAN own) RMA files generated by MEGAN from BLAST files. To learn how to create an RMA file from a  file of reads and a BLAST file, we will use the following two raw input files:




- D. H. Huson, A. Auch, J. Qi, and S. C. Schuster. MEGAN analysis of metagenomic  data. Genome Research, 17:377–386, 2007.

- P. J. Turnbaugh, R. E. Ley, M. A. Mahowald, V. Magrini, E. R. Mardis, and J. I. Gordon.
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122):1027–1031, Dec 2006.
- P. J. Turnbaugh, F. Backhed, L. Fulton, J. I. Gordon. Diet-induced obesity is linked to marked but
reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213-223, Apr 2008.

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