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MEGAN specifications


Unique identifier OMICS_01516
Alternative names MEtaGenome ANalyzer, MEGAN6, MEGAN5
Software type Package/Module, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 6.8.14
Stability Stable
Maintained Yes


  • MEGAN-LR (Long Read extension of the metageno




No version available



  • person_outline Daniel H. Huson
  • person_outline Benjamin Albrecht
  • person_outline Caner Bagci
  • person_outline Irina Bessarab

Additional information

A free edition (Community Edition) and a paid edition (Ultimate Edition) are both available.

Publications for MEtaGenome ANalyzer

MEGAN citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] removal. The reads of the control samples were analyzed using Diamond blastx () against the nonredundant protein database of NCBI (nr, November 2015 version). The blast results were visualized using MEGAN6 Community Edition (). An extra contaminant file was created with the complete genomes of species present at over 1,000 reads in the positive- and negative-control samples. Then, bowtie2 () was […]


What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] agenome were normalized to the lowest number of sequences containing predicted proteins with known function (6,785,276). The structure and abundance of the functional subsystems were visualized using metagenome ANalyzer5 (MEGAN) () and in the latter compared with the relative distribution of bacterial functions. For further analysis of the distribution of the archaeal genes among the domain Archae […]


Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non suppressive Soils for Rhizoctonia solani AG8

Front Microbiol
PMCID: 5945926
PMID: 29780371
DOI: 10.3389/fmicb.2018.00859

[…] non-suppressive libraries and 227 in the suppressive libraries (Table ).The taxonomic annotation of the DE contigs was examined using the BLASTX annotation of NCBI nr (as for the unassembled reads in MEGAN). The majority of contigs were bacterial (1499/1855 contigs; 81%) while archaea and eukaryotes represented <1% each (14 contigs) (Table ). Contigs with greater expression in the non-suppressive […]


Highly Promiscuous Oxidases Discovered in the Bovine Rumen Microbiome

Front Microbiol
PMCID: 5945886
PMID: 29780372
DOI: 10.3389/fmicb.2018.00861

[…] It was impossible to accurately assign the three metagenomic inserts from a taxonomical point of view, as their sequences were too distant from any available sequenced genome. A MEGAN analysis using low stringent criteria revealed that the sequences were probably derived from Firmicute bacteria. Indeed, 6/28, 9/18, and 5/29 ORF sequences from Clones 1, 2, and 3, respectively, […]


Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] All UDG-treated samples derived from teeth (n=68) were screened for their metagenomic  content with the alignment tool MALT and the metagenome analyzer MEGAN []. After pre-processing, as described above, MALT v0_3_6 was used to align all samples against a collection of all complete bacterial genomes in FASTA format downloaded from […]


Microbiome Dynamics in a Large Artificial Seawater Aquarium

Appl Environ Microbiol
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] emoved from the merged reads by using RiboPicker (). Non-rRNA reads were queried against the NCBI nr database with DIAMOND (), using BLASTX and a minimum bit score of 50. The output was imported into MEGAN Community Edition version 6.8.20 () for taxonomic assignment. To compare relevant genes and taxa between time points, the sample 0928 transcriptome was randomly subsampled to the same number of […]


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MEGAN institution(s)
Center for Bioinformatics, University of Tübingen, Tübingen, Germany

MEGAN review

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Works well with DIAMOND for metatranscriptomic data analysis.