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informatic expertise?

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The microbial metagenomic trait statistical analysis workflow calculates a number of ecologically interesting traits of bacterial communities as observed by high throughput metagenomic DNA sequencing. These metagenomic traits workflows are significant, as it is very likely that environmental sequencing in natural and disturbed habitats will become a routine part of monitoring programs.

Who is it for?

Users who have microbial metagenomic DNA sequence data.

What is it for?

This workflow allows standardized, repeatable, and comparable utilization of metagenomic data while hiding the complexity of analytical procedures behind well-defined web services.

How does it work?

The Microbial Metagenomic Trait Statistical Analysis workflow computes the multivariate statistics related to the metagenomic community traits outlined in Barberan et al. (2012) "Exploration of community traits as ecological markers in microbial metagenomes" (DOI: 10.1111/j.1365-294X.2011.05383.x). The traits included in the statistical analyses range from GC-content to functional diversity, and deliver a valuable set of ecological markers in order to discriminate between habitats or geographic locations. Furthermore, inter-trait relationships can be used as habitat descriptors or indicators of artifacts during sample processing. Overall, these metagenomics community traits approach, here combined in a single workflow, helps to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.

Expected results

Data for each trait and summarizing statistics.

Links to workflows and user documentation

Workflow for the full calculation and statistical analysis of all traits of a new quality controlled metagenome

Workflow for the statistical analysis of pre-calculated metagenomic traits

Documentation

Example of use

The workflow was used to build the Metagenomic Trait Database (http://mb3is.megx.net/mg-traits).

Analysis of sequenced water samples from Ocean Sampling Day, a world-wide coordinated microbial sequencing initiative of ocean habitats.

metagenomics-trait-wf


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News

19 February 2015

At the final review of the project by the EC, one of the reviewers said: “Incredible work done with a community that is not unified. Remarkable work. It opens for new development in a near future. Hope for success. Good project. Happy that you have been financed three plus years ago.”

Read all about the project and its results in the Project Final Report or read the Executive Summary only.