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.

Environment Modules¶

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

Environment Variables¶

HPC_MEGAN_DIR - software directory

Categories¶

biology, ngs