We have implemented a number of tools in the MBAC Galaxy Portal to support a Systems Biology approach to the analysis of the Metabiome (the interactions of the Microbiome, Metabolome, and Immunome). These include tools to calculate Correlation Netwoks for complex data matrices and for calculating the statistically significant differences (Correlation Difference) of two Correlation Networks. The networks can be visualized in Cytoscape.
This approach visualizes potential interactions between the microbiome, metabolome, and immunome. One can then generate new hypothesis (i.e. knowledge discovery) that can then be used for hypothesis driven experimental models.
We have implemented a local version of Qiime in the MBAC Galaxy Portal.
Qiime (Quantitative Insights Into Microbial Ecology) is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.
04/12/2013 We added PICRUSt (0.9.1) tools for the prediction metagenome functional content from 16S rRNA. This includes tools for manipulating BIOM formatted matrices.
04/25/2013 Qiime Version 1.6.0 has been installed.
04/25/2013 Qiime Tutorial for basic workflow.
05/01/2013 Updated Parameter File documentation for Qiime 1.6.0
05/01/2013 Scripts Documentation for Qiime 1.6.0
05/01/2013 Updated Documentation for Qiime 1.6.0
MEGAN 4 – MEtaGenome ANalyzer
In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of environmental sequencing projects. Thus, there is a dramatic increase in the volume of sequence data to be analyze
Login to the MBAC server through your local MBAC account to pipe compressed Xview to your terminal:
ssh -X -C email@example.com
And then run MEGAN:
SESAME SNP Analysis
|SE|S|AM|E| Barcode is a user-friendly web application for barcoding amplicon sequences obtained through NGS. The software automatically processes DNA sequences datasets, sorting for multiplexed loci and samples identified by oligonucleotide tags, and allows for the assignment of sequences to a preloaded reference library (from Genbank to in-house scale). The results are displayed both as samples-based synthetic tables and graphical representations. The deliveries of |SE|S|AM|E| Barcode was developed with multiple applications in mind, such as specimen assignment to species referenced in DNA libraries, molecular characterization of trophic networks or more generally metagenomics and environmental barcoding studies.