16SrRNA Microbiome Intermediate Bioinformatics Training

    Dates for the Course: August to October 2019 (exact dates and times to be confirmed)

    Venue of the Course: Successful hosting classrooms (we have 26 registered classrooms)

    Course Organizers: Verena Ras, Gerrit Botha, Shaun Aron, Sumir Panji, Nicola Mulder

    Course Overview:  The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.

    The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a blended learning approach similar to the popular H3ABioNet Introduction to Bioinformatics Training (IBT) through the use of a combination of theoretical and practical sessions in order for participants to gain knowledge in the use of various tools and resources needed for 16S rRNA microbiome data analysis. There will be 2 contact sessions per week consisting of both theoretical and practical coursework. Participants will generally watch pre-recorded videos in their classrooms (theory) followed by a practical exercise for the remainder of the session. Contact sessions will generally be 4 hours each however the exact format and length of classes will be communicated in due course. 

    Course Objectives: By the end of the course participants should be able to:

    • Describe the importance of the microbiome and why it should be studied
    • Understand how to design 16S rRNA microbiome studies
    • Be able to apply basic syntax and operations in R
    • Understand the different NGS data types (e.g. MiSeq reads) produced for a 16S rRNA microbiome study
    • Evaluate the quality of NGS sequence reads and samples
    • Understand the various bioinformatics tools used for 16S microbiome studies
    • Understand the various 16S rRNA bioinformatics pipelines being used to study the microbiome.
    • Apply the H3ABioNet’s 16S rRNA pipeline and understand how to execute this
    • Understand the use of workflow languages (Nextflow) and containerized images (Singularity) to automate analyses
    • Analyze 16S rRNA microbiome data and interpret results

    Intended Audience: Anyone who will be working with 16S rRNA microbiome data and would like to learn more about the bioinformatics analyses.

    Syllabus and Tools:

    • Introduction to the Linux command line / intro to R
    • Introduction to the microbiome and study design – why 16S?
    • Sample collection, extraction and library prep for 16S NGS analyses
    • 16S rRNA gene amplicon sequencing bioinformatics pipeline: the theory
    • 16S analysis pipeline - QC, ASV picking, taxonomic classification and alignment
    • Downstream analysis in R - using the packages phyloseq, NMF, vegan, metagenomeSeq (among others)
    • Potential bonus module: Shotgun sequencing

    Participant application date opens: 17 July 2019

    Participant application date closes: 14 August 2019

    Link to participant application form: https://is.gd/intbt_participant_application

    Prerequisites (for participants): As this is an intermediate course, some familiarity with the Unix command line and R scripting will be assumed. However, should participants wish to gain some background knowledge before the start of the course, the following tutorials will provide a good foundation. 

    Linux: http://www.ee.surrey.ac.uk/Teaching/Unix/

    R: https://www.statmethods.net/r-tutorial/index.html

    R: https://www.datacamp.com/courses/free-introduction-to-r 

    Workshop limitations: This workshop provides an overview and guidance on 16S rRNA microbiome analyses and will provide you with the ability to perform a variety of analyses on microbiome data. The course however will not teach any advanced programming or go into depth with R or Unix. Participants are encouraged to explore these tools in greater depth independently.

    Click here to go to main course site

     

    2019 Course Resources:

    Lecture Slides:

    * all lecture slides loaded in .pdf format

    Module 1: Introduction to unix and R

    Introduction to Unix
    Introduction to R

    * Trainers: Gerrit Botha & Katie Lennard

    Module 2: Introduction to the Microbiome - why 16S

    Part 1
    Part 2
    Part 3

    * Trainer: Shantelle Claassen-Weitz

    Module 3: Sample Collection, extraction and library prep for 16S NGS analyses

    Part 1
    Part 2
    Part 3
    Part 4
    Part 5

    * Trainer: Shantelle Claassen-Weitz


    Module 4: 16S rRNA sequencing bioinformatics pipeline: the theory

    Module 4 - pipeline theory

    * Trainer: Kilaza Samson Mwaikono

    Module 5: 16S rRNA analysis pipeline - QC, OTU picking/ASV analysis, classification, alignment, Usearch and QIIME

    Module 5 - dada2 pipeline

    *Trainer: Imane Allali

    Module 6: Downstream analysis in R - Phyloseq, NMF

    Module 6 - Downstream analysis in R

    * Trainer: Katie Lennard

    Additional slides:

    Introduction Week slides (*Trainer: Verena Ras)

    Staff Training Week slides (*Trainers: Verena Ras & Gerrit Botha)

    Wrap-up Week slides (*Trainer: Verena Ras)


    Other Materials and resources:

    YouTube channel housing lecture videos: click here 

    Course GitHub sites (code and scripts):


    Training containers:


    Workflow repository:  The workflow is open-source (MIT licence) and available on GitHub: https://github.com/h3abionet/TADA

    Practice dataset: click here

     

     


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