Metagenomics is a discipline that enables the genomic study of uncultured microorganisms
Before diving into this topic, we recommend you to have a look at:
|Lesson||Slides||Hands-on||Input dataset||Workflows||Galaxy tour||Galaxy instances|
|Introduction to metagenomics||slides|
|16S Microbial Analysis with Mothur||tutorial Toggle Dropdown||zenodo_link||workflow||interactive_tour||instances|
|Analyses of metagenomics data - The global picture||tutorial Toggle Dropdown||zenodo_link||workflow||interactive_tour||instances|
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -d -p 8080:80 quay.io/galaxy/metagenomics-training
It will launch a flavored Galaxy instance available on http://localhost:8080.
This material is maintained by:
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:
- John C. Wooley, Adam Godzik, Iddo Friedberg: A Primer on Metagenomics
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology
- Robert C. Edgar, Brian J. Haas, Jose C. Clemente, Christopher Quince, Rob Knight.: UCHIME improves sensitivity and speed of chimera detection
- Holly Bik and Pitch Interctive Inc.: Phinch: An interactive, exploratory data visualization framework for -omic datasets
- Brian D Ondov, Nicholas H Bergman, Adam M Phillippy: Krona: Interactive Metagenomic Visualization in a Web Browser
- Finotello F, Mastrorilli E, Di Camillo B.: Measuring the diversity of the human microbiota with targeted next-generation sequencing.
- Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra: Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.
- Patrick D Schloss: Secondary structure improves OTU assignments of 16S rRNA gene sequences.