This course was delivered as an ONLINE COURSE for remote participation 
due to the COVID-19 measures enforced by most European governments.

Description

This online course introduces the participants to microbiome analysis methods, tools, and file formats. It covers the whole workflow from quality control and filtering to quantification and statistical analysis using Mothur and Phyloseq tools integrated in the user-friendly Chipster platform. Please note that this course focuses on microbiome analysis of amplicon sequencing data (as opposed to metagenomics where all the genes are sequenced).

The course consists of lectures and practical exercises. The lectures will be available as short videos, and the participants are requested to view them prior to the course. This gives you more time to reflect on the concepts so that you can use the course days more efficiently. The lectures are summarized and questions answered during the course.

Learning outcome

After this course, you will be able to

preprocess amplicon sequencing data for microbial community analysis


compare the structure of microbial communities using ordinations and multivariate statistics

Prerequisites and content level

The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required.

The content level of the course is intermediate and the course is intended for life scientists who are planning to use 16S or other amplicon sequencing in their microbiome research. This course is suitable also for those researchers who do not plan to analyze data themselves, but who need to understand the concepts in order to discuss with bioinformaticians.

Agenda

Day 1, Thursday May 20 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)

Checking the quality of reads with MultiQC


Preprocessing 



    combining paired reads to contigs


    screening sequences for length and ambiguous bases


    removing identical sequences




Alignment



    aligning sequences to the Silva reference alignment


    screening aligned sequences for alignment position and homopolymers


    filtering alignment for empty columns and overhangs


    removing new identical sequences




Preclustering, removing chimeric sequences

Day 2, Friday May 21 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)

Data tidying and analysis

Creating and importing phyloseq input files



    Including taxonomic assignments and OTU clustering




Data inspection and tidying using phyloseq



    Removing unwanted taxa


    Filtering singletons and doubletons


    Prevalence filtering




Data transformation, ordination and conversion



    CLR, Hellinger and % relative abundance


    nMDS and db-RDA


    DESeq2 format conversion and variance-stabilising transformation




Relative abundance plots


Community comparisons using PERMANOVA, PERMDISP and DESeq2

Lecturers: 

Dr. Jesse Harrison (CSC), Dr. Eija Korpelainen (CSC)

Language:  English
Price:           Free of charge (2 training days)
https://events.prace-ri.eu/event/1198/