Difference between revisions of "MEGAN"
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| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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. | ||
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Revision as of 14:04, 13 June 2022
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.
System Variables
- HPC_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.