Educational Resources for for Amplicon Metagenomics

Articles

1. mothur and QIIME
   • Description: Very nice article that describes how mothur and QIIME are different and/or similar.
   • Link: http://blog.mothur.org/2016/01/12/mothur-and-qiime

Workshops

1. 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
2. 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

1. 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

2. 16S Metagenomic Analysis Tutorial

   • Description: In this tutorial we will explore the primary characterization of a specific human gut microbiome dataset, namely the enterotype dataset from…
   • Link: http://web.evolbio.mpg.de/~wang/Site/R_tutorial_files/16S Metagenomic Analysis Tutorial.pdf

3. 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
   • Description: Explore the goals, approaches, and challenges for creating phylogenetic trees, or phylogenies.
   • Link: http://readiab.org/book/0.1.3/2/4 2. Studying Microbial Diversity
   • Description: Explore terminology, methods and approaches for performing microbial diversity analysis.
   • Link: http://readiab.org/book/0.1.3/3/1

4. Microbiome data analysis

   • Description: The purpose of this tutorial is to describe the steps required to perform microbiome data analysis, explain how to build your own data flow, and finally, discuss the results obtained in such analysis.
   • Link: https://genestack-user-tutorials.readthedocs.io/tutorials/Microbiome_analysis

1. QIIME2 Tutorials

   1. QIIME2 Glossary
   2. Description: It is important to first know QIIME2 terminology before starting to learn it.
   3. Link: https://docs.qiime2.org/2019.1/glossary
   4. Overview of QIIME2 Plugin Workflows
   5. Description: After terminology this tutorial is your first step to learn QIIME2.
   6. Link: https://docs.qiime2.org/2019.1/tutorials/overview/
   7. Microbiome Analysis with QIIME2: A Hands-On Tutorial[Presentation]
   8. Description: Nice tutorial for introduction to QIIME2
   9. Link: http://compbio.ucsd.edu/wp-content/uploads/2018/07/20180621_oslo_university_microbiome_analysis_with_qiime2_tutorial.pdf
   10. “Moving Pictures” tutorial [VeryNiceTutorial!]
   11. 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.
   12. Link: https://docs.qiime2.org/2019.1/tutorials/moving-pictures
   13. QIIME2 workflow
   14. Description: Using the Quantitative Insights Into Microbial Ecology (QIIME2) software pipeline for analysis of marker gene-based microbiome sequencing data
   15. Link: https://chmi-sops.github.io/mydoc_qiime2.html

2. Amplicon Metagenomics

   • Description: This tutorial describes a strategy for assembling, filtering and analysing an NGS metagenomic data set in Geneious Prime.
   • Link: https://www.geneious.com/tutorials/metagenomic-analysis

3. Taxonomy from species name in R

   • Description: This tutorial describes one of many approaches to generate phylogenetic tree from specie names.
   • Link: https://taylorreiter.github.io/2017-07-28-Taxonomy-from-Species-Name-in-R