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Getting Started

Getting started with MEGAN6

Overview  What's New  Features  Getting Started  Download  Buy & Upgrade 

Installation and Startup


Visit the download page to download the installer that is appropriate for the operating system that you are using. Please note that 32-bit operating systems are not supported. Double-click on downloaded installer to start the installation process. Complete the installation process. 

Example data


MEGAN6 files containing metagenome or metatranscriptome datasets are usually very big, often tens of gigabytes in size. Hence, no sample data is shipped with the program. Instead, you can open one or more datasets from the MEGAN server website, using the File->Open From Server menu item. Simply double-click on one of the file names listed in the file window and it will open in MEGAN6.

By default, MEGAN6 will open a file in its main taxonomic viewer. To see the functional content of a sample, as classified by SEED, say, press the SEED button in the toolbar.

For further instructions on how to use the program, see the the manual.

Preparing your own data

MEGAN6 is a tool for the exploration and visualization of microbiome data. However, before data can be opened in MEGAN, the raw sequencing data has to be preprocessed. Preprocessing involves a number of steps.
First, the sequencing reads are usually subjected to quality control, which involves adaptor removal, trimming of low quality regions and removal of low-quality reads. (Which these steps are clearly necessary for some computational questions such as assembly, there is little evidence that this is necessary when performing comparison-based metagenome analysis). 
Second, the reads that pass quality control must be compared against an appropriate reference database. One approach is to compare the reads against he NR database using a BLASTX-like computation. The fastest program for performing this computation is DIAMOND.
DIAMOND creates a DAA ("Diamond alignment archive") file as output. To work with the output of DIAMOND in MEGAN, you must do one of two things:
Import the DAA file into MEGAN using MEGAN's File->Import From Blast... dialog. This will generate a MEGAN6 "RMA" file that can used to interactively explore the data. Alternatively, use the command line tool called "meganizer" to analyze and index, i.e. "meganize", the DAA file. It can then be directly opened in MEGAN6. The latter option is faster than the former and saves disk space as no additional file is generated.
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