Microbial Metagenomic Trait Statistical Analysis Workflow
Created: 2012-12-19 23:11:08
Last updated: 2014-11-12 09:45:08
This workflow retrieves the following microbial metagenomic traits from the Microbial Metagenomic Trait Database:
-GC content
-Variance of GC content
-Dinucleotides
-Number of rRNA
-Codon usage
-Amino acid composition
-Acidic to basic amino acids ratio
-% of Transcriptional factors
-% of classified reads
-Functional content
-Functional diversity
-Taxonomic content
-Taxonomic diversity
After the retrieval performs the ecological analyses described in Barberan et al. 2012 (http://dx.doi.org/10.1111/j.1365-294X.2011.05383.x)
Please read: https://wiki.biovel.eu/display/doc/Metagenomic+Workflows
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
| Antonio Fernandez-Guerra, Pelin Yilmaz and Renzo Kottmann |
Titles (1)
| Microbial Metagenomic Trait Statistical Analysis Workflow |
Descriptions (1)
| This workflow retrieves the following microbial metagenomic traits from the Microbial Metagenomic Trait Database:
-GC content
-Variance of GC content
-Dinucleotides
-Number of rRNA
-Codon usage
-Amino acid composition
-Acidic to basic amino acids ratio
-% of Transcriptional factors
-% of classified reads
-Functional content
-Functional diversity
-Taxonomic content
-Taxonomic diversity
After the retrieval performs the ecological analyses described in Barberan et al. 2012 (http://dx.doi.org/10.1111/j.1365-294X.2011.05383.x)
Please read: https://wiki.biovel.eu/display/doc/Metagenomic+Workflows |
Dependencies (0)
Inputs (1)
| Name |
Description |
| mg_list |
A list or file of metagenomes present in the Microbial Metagenomic Trait Database (http://mb3is.megx.net/mg-traits)
Select the metagenomes and downlad the file list from http://blast2.mpi-bremen.de/mg-traits/samples
To run the workflow, at least select more than 10 metagenomes.
|
Processors (2)
| Name |
Type |
Description |
| retrieve_traits |
workflow |
|
| Metagenomic_Traits_S |
workflow |
|
Outputs (19)
| Name |
Description |
| phyloMantel |
Mantel test against phylogenetic distance matrix (controlling for functional response)
|
| funcMantel |
Mantel test against functional distance matrix (controlling for phylogenetic response)
|
| summary_traits |
A table with all the traits used in this statistical analysis.
|
| pcaLog |
Log file from the PCA analysis
|
| traits_biplot |
PCA biplot.
|
| bivariatePlot |
All against all trait realtionships.
|
| traitsPCAPlot |
Plot of the PCA of all traits.
|
| funcNMDSLog |
Log file from the functional NMDS
|
| taxoNMDSLog |
Log file from the functional NMDS
|
| funcNMDSTxt |
Data used for the functional NMDS plot
|
| taxoNMDSPlot |
Plot of the taxonomic NMDS
|
| funcNMDSPlot |
Plot of the functional NMDS
|
| taxoNMDStxt |
Data used for the taxonomic NMDS plot
|
| aa_content |
Aminco Acid content ot the metagenomes.
|
| codon_usage |
Codon Usage data of the metagenomes.
|
| di_nucleotide_odds_ratio |
Di-nucleotide odds-ration data of the metagenomes.
|
| functional_content |
Functional content data of the metagenomes.
|
| simple_traits |
Simple triats data of the metagenomes.
|
| taxonomic_content |
Taxonomic content of the metagenomes.
|
Datalinks (26)
| Source |
Sink |
| mg_list |
retrieve_traits:mg_list |
| retrieve_traits:dinuc |
Metagenomic_Traits_S:dinuc |
| retrieve_traits:functional_content |
Metagenomic_Traits_S:func |
| retrieve_traits:aa |
Metagenomic_Traits_S:aa |
| retrieve_traits:simple_traits |
Metagenomic_Traits_S:traits |
| retrieve_traits:taxonomic_content |
Metagenomic_Traits_S:phylo |
| retrieve_traits:codon |
Metagenomic_Traits_S:codon |
| Metagenomic_Traits_S:phyloMantel |
phyloMantel |
| Metagenomic_Traits_S:funcMantel |
funcMantel |
| Metagenomic_Traits_S:summary_traits |
summary_traits |
| Metagenomic_Traits_S:pcaLog |
pcaLog |
| Metagenomic_Traits_S:traitsBiplot |
traits_biplot |
| Metagenomic_Traits_S:bivariatePlot |
bivariatePlot |
| Metagenomic_Traits_S:traitsPcaPlot |
traitsPCAPlot |
| Metagenomic_Traits_S:funcNMDSLog |
funcNMDSLog |
| Metagenomic_Traits_S:phyloNMDSLog |
taxoNMDSLog |
| Metagenomic_Traits_S:funcNmdsTxt |
funcNMDSTxt |
| Metagenomic_Traits_S:phyloNmdsPlot |
taxoNMDSPlot |
| Metagenomic_Traits_S:funcNmdsPlot |
funcNMDSPlot |
| Metagenomic_Traits_S:phyloNmdsTxt |
taxoNMDStxt |
| retrieve_traits:aa |
aa_content |
| retrieve_traits:codon |
codon_usage |
| retrieve_traits:dinuc |
di_nucleotide_odds_ratio |
| retrieve_traits:functional_content |
functional_content |
| retrieve_traits:simple_traits |
simple_traits |
| retrieve_traits:taxonomic_content |
taxonomic_content |
Uploader
License
All versions of this Workflow are
licensed under:
Version 9 (latest)
(of 9)
Credits (4)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (2)
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (1)
(Workflows/Files)
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Download Workflow
]
Reviews
(0)
No comments yet
Log in to make a comment