Metagenomics is a discipline that enables the genomic study of uncultured microorganismsYou can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.
Before diving into this topic, we recommend you to have a look at:
Introduction to metagenomics
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16S Microbial Analysis with mothur (extended)
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16S Microbial Analysis with mothur (short)
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|16S Microbial analysis with Nanopore data||tutorial Toggle Dropdown|
Analyses of metagenomics data - The global picture
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|Antibiotic resistance detection||tutorial Toggle Dropdown||
|Identification of the micro-organisms in a beer using Nanopore sequencing||tutorial Toggle Dropdown|
|Metatranscriptomics analysis using microbiome RNA-seq data||plain text Toggle Dropdown||tutorial Toggle Dropdown||
|Metatranscriptomics analysis using microbiome RNA-seq data (short)||tutorial Toggle Dropdown|
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 -p 8080:80 quay.io/galaxy/metagenomics-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked QuestionsCommon questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.
This material is maintained by:Bérénice Batut Saskia Hiltemann
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:Bérénice Batut Saskia Hiltemann Dave Clements Cristóbal Gallardo Willem de Koning Pratik Jagtap Subina Mehta Ray Sajulga Emma Leith Praveen Kumar
- 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
- 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.