Difference between revisions of "MEGAN"

Latest revision as of 15:38, 15 April 2024

Description

MEGAN6 (MEtaGenome ANalyzer) is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
Bar charts, word clouds, and many other charts
PCoA, clustering and networks
Supports metadata
MEGAN parses many different types of input

Environment Modules

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

System Variables

HPC_MEGAN_DIR - installation directory
HPC_MEGAN_BIN - executable directory

Additional Information

To run the MEGAN6 GUI to process your data, launch an interactive session in Open on Demand (or use your GPU allocation) and type the following command:

$ module load megan

$ MEGAN

Usage Manual for MEGAN6: https://software-ab.cs.uni-tuebingen.de/download/megan6/manual.pdf

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|megan}}
-|{{#vardefine:url|http://ab.inf.uni-tuebingen.de/software/megan/}}
+|{{#vardefine:url|http://ab.inf.uni-tuebingen.de/software/megan6/}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-MEGAN  - MEta Genome ANalyzer - is a tool for metagenomic analysis of short-read data. MEGAN's functionality includes:
+MEGAN6 (MEtaGenome ANalyzer) is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools
+you need in one application.
-* 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.
+* Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
+* Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
+* Bar charts, word clouds, and many other charts
+* PCoA, clustering and networks
+* Supports metadata
+* MEGAN parses many different types of input
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 53: / Line 41: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+To run the MEGAN6 GUI to process your data, launch an interactive session in Open on Demand (or use your GPU allocation) and type the following command:
+$ module load megan
+$ MEGAN
+Usage Manual for MEGAN6:
+https://software-ab.cs.uni-tuebingen.de/download/megan6/manual.pdf
 |}}