Microbial community / environmental DNA analysis with Chipster

This online hands-on course focuses on amplicon-based community analysis methods. They are introduced using microbial communities as an example, but the methods are applicable to environmental DNA (eDNA) studies of other organisms as well.

This course covers the whole workflow from quality control and filtering to quantification and statistical analysis using DADA2 and Phyloseq tools integrated in the user-friendly Chipster software. Note that while this course focuses on amplicon sequence variant (ASV) -based analysis, Chipster contains also Mothur-based tools for OTU-based analysis.

The course consists of lectures and practical exercises. The lectures will be available as short videos, which participants are requested to view 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.

Both course days are 9:00-13:00 in Zoom.

Learning goals

After this course, you will be able to
– preprocess amplicon sequencing data for community analysis
– compare the structure of communities using ordinations and multivariate statistics

Prerequisites and target audience

The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required.
The course is intended for life scientists who are planning to use 16S or other amplicon sequencing in their 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

• Checking the quality of reads with MultiQC
• Removing primers with Cutadapt
• Processing reads into amplicon sequence variants (ASVs) in DADA2:
  • Filter and trim reads
  • Learn error rates and infer sample composition
  • Make ASV table and remove chimeras
  • Assign taxonomy
• Creating phyloseq object

Day 2

• Data inspection and tidying using phyloseq
  • Removing unwanted taxa
  • Prevalence filtering
• Relative abundance plots
• Alpha diversity, rarefaction curve
• Data transformations
  • % relative abundance, centered log ratio and Hellinger transformations
• Community comparisons
  • Ordination with nMDS and db-RDA
  • Hypothesis testing with PERMANOVA and PERMDISP
• Differential abundance analysis with DESeq2

Registration

Please fill in the registration form by 1.4.2026. If the course gets booked out earlier, you will be added in the waiting list and informed if a place becomes available. The course is kindly sponsored by ELIXIR Finland, so it is free of charge for the participants.

Trainers

Heli Juottonen and Eija Korpelainen (CSC)