Educational Resources for for Amplicon Metagenomics
Updated on: 03 Sep 2019
Articles
- mothur and QIIME
Workshops
- CoDaSeq workshop
- Description: The intention of this workshop is to give
participants a background in Compositional Data Analysis (CoDa)
for transcription studies. At the end of the workshop you will
have been introduced to CoDa, why you’d use CoDa, and gain
hands-on experience using CoDa analysis in R.
- Link:
https://github.com/ggloor/CoDa_microbiome_tutorial/wiki
- Microbiota Analysis in R [workshop/tutorial]
- Description: The goal of this tutorial is to demonstrate
basic analyses of microbiota data to determine if and how
communities differ by variables of interest. In general, this
pipeline can be used for any microbiota data set that has been
clustered into operational taxonomic units (OTUs).
- Link: https://rpubs.com/dillmcfarlan/R_microbiotaSOP
Tutorials
- Microbiota Procesing in mothur: standard operating procedure
(SOP)
- Description: The goal of this tutorial is to demonstrate
standard operating procedures (SOP) for processing amplicon data
that are generated using Illumina’s MiSeq platform with paired
end reads.
- Link: https://rpubs.com/dillmcfarlan/mothurSOP
- 16S Metagenomic Analysis Tutorial
- An Introduction to Applied Bioinformatics[OnlineBook]
- Description: An Introduction to Applied Bioinformatics (or
IAB) is a free, open source interactive text that introduces
readers to core concepts of bioinformatics in the context of
their implementation and application.
- Link: http://readiab.org
Focus mainly on following chapters
- Phylogenetic reconstruction
- Microbiome data analysis
-
QIIME2 Tutorials
- QIIME2 Glossary
- Overview of QIIME2 Plugin Workflows
- Microbiome Analysis with QIIME2: A Hands-On
Tutorial[Presentation]
- “Moving Pictures” tutorial [VeryNiceTutorial!]
- Description: In this tutorial you’ll use QIIME 2 to
perform an analysis of human microbiome samples from two
individuals at four body sites at five timepoints, the first
of which immediately followed antibiotic usage.
- Link:
https://docs.qiime2.org/2019.1/tutorials/moving-pictures
- QIIME2 workflow
- Amplicon Metagenomics
- Taxonomy from species name in R
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