MEGAN

Description

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.

Run module spider megan to find out what environment modules are available for this application.

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.