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MEGAN - MEta Genome ANalyzer - is a tool for metagenomic analysis of short-read data. MEGAN's functionality includes:

  • COG/EGGNOG analysis: MEGAN5 can map reads to COG/EGGNOG classes and provides analyzer window.
  • Update of SEED and KEGG mapping data: MEGAN5 is shipped with new SEED and KEGG mapping files. The KEGG pathways shipped with MEGAN are based on the last free version of KEGG (June 2011).
  • PCoA analysis of taxonomy and function: MEGAN5 allows the user to perform PCoA analysis based on taxonomy for function, the latter based on SEED, KEGG or COG/EGGNOG.
  • MEGAN5 makes it easy to work with many different samples simultaneously. A MEGAN5 comparison document can contain any number of samples. Samples can be extracted, merged or resampled.
  • Biome extraction: MEGAN5 provides methods for computing the core biome, total biome, minimal biome and rare biome for a set of samples.
  • Metadata: MEGAN5 supports metadata associated with samples. Such attributes can be used to select, order or color samples.
  • Charting: MEGAN5 contains a number of new charts including a radial space filling trees, bubble charts, word clouds and co-occurrence graphs.
  • Improved LCA algorithm: novel "minimum taxon cover" algorithms greatly enhances the specificity of the taxonomic LCA placement algorithm.
  • Color management: MEGAN5 always assigns the same colors to the same entities across different windows and datasets. The program uses built-in palette, however, the user can interactively chance any choice.

Required Modules


  • megan

System Variables

  • HPC_{{#uppercase:megan}}_DIR - installation directory

Additional Information

Please run MEGAN in the command-line mode when processing your data, so you could run it inside a batch job. Run

$ module load megan
$ MEGAN -h

to see all command-line options.


  • Validate 4/5/2018