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Other Resources

Overview

Teaching: 5 min
Exercises: 0 min
Questions
  • Where are other metagenomic resources?

  • How can lessons be previewed?

Objectives
  • Know some places where to find more information.

Other resources

Cuatro Ciénegas

More information about 4 Ciénegas is available in these podcasts Mexican oasis in the desert and Mexican Oasis, in this Cuatro Ciénegas Video, and finally in the manuscript Cuatro Ciénegas.

Other tutorials and books

Now that you finished this metagenomic lesson, you are ready to explore on your own the universe of available tutorials. Phyloseq tutorial contains much more examples of metagenomic data manipulation.
The Computational Genomics tutorial by Schmeir explains carefully each step of the process. To know more about metagenomics history in the Meren Lab blog there is a wonderful entry called History of metagenomics as well as several videos explaining Metapangenomics: A nexus between pangenomes and metagenomes, The power of metagenomic read recruitment, Genome-resolved metagenomics: key concepts in reconstructing genomes from metagenomes. Finally, for spansih speakers the ISME course is a detailed tutorial for 16s metabarcoding ISME Análisis de diversidad.

The book Microbiomes shares a contemporary concept of the microbiomes. Books Statistical analysis of microbiome data and statistical analysis of microbiome data with r contain a state of the art compendium of the statistical and computational microbiome analysis techniques beyond diversity analysis.

Other studies and databases

Some databases are: jgi, The Earth microbiome project, metaSUB, The atlas of soil microbiome, and The Human microbiome project.

MG-RAST

A useful and easy to use resource is MG-RAST, is at the same time a database and an online analysis tool. MG-RAST is an online metagenomic platform where you can upload your raw data with its corresponding metadata and get a full taxonomic analysis of it. MG-RAST is a great place to get started in this type of analyzes and it is also a big repository of available data for future experiments. On the downside, it is not possible to greatly modify the steps and parameters in the MG-RAST workflow, so there is not much room when it comes to implementing our preferred analysis tools when using MG-RAST.

The Cuatro Ciénegas data that we used in the workshop is already in MG-RAST! You can check it out here.

We can check the taxonomical distribution of our sample at different taxonomical level.

The most abundant phylum is Proteobacteria.
Pie chart showing the relative abundance at phylum level, and the legend with the phylum names, read count and percentages.

Since we have a shotgun metagenome, we can also investigate the metabolic functions present in our sample. MG-RAST can find genes and annotate their function through an implementation of RAST, or Rapid Annotation using Subsystems Technology. By looking at the charts generated by this analysis, we see that most of the genes are dedicated to metabolism.

Pie chart showing the relative abundance of general functional categories, and the legend with the category names, read count and percentages.

Pie chart showing the relative abundance of specific functional categories, and the legend with the category names, read count and percentages.

MG-RAST has it’s own specific pipeline, so it is a very useful tool to have a quick look of your data, and also to store it and share it!, but it does not keep you from making your own personalized analysis like we just learn!

Discussion: Exploring more resources

Explore one of the suggested resources and discuss your findings with a neighbor.

Carpentries Philosophy

A good lesson should be as complete and clear that becomes easy to teach by any instructor. Carpentries lessons are developed for the community, and now you are part of us. This lesson is being developed and we are sure that you can colaborate and help us improve it.

Key Points

  • Enjoy metagenomics.