This workshop is conducted in English.

This workshop is designed for researchers with prior experience in amplicon sequencing or those who have completed an introductory course in the field. The session will commence with a presentation focusing on the nuances of amplicon sequencing data analysis, incorporating tools such as Usearch, Vsearch, and qiime2. Topics covered will include quality control, sequence alignment, initial filtering, normalization, and advanced analyses such as diversity metrics and taxonomic assignment.

Our teaching approach emphasizes hands-on learning through practical examples, exercises, and a dedicated case study. The primary objective is to impart practical knowledge essential for effective amplicon sequencing analysis. The workshop will be interactive, featuring progress checks and opportunities for participants to ask questions.

Upon completion of the workshop, participants will receive a certificate affirming their attendance and successful engagement in the amplicon sequencing analysis course.

Date: March 23 and 24, 2025, 10:00 a.m. – 3:00 p.m. (2-days online workshop).

Time: 10 hours (5 hours each day with a coffee break).

Location: online.

Group: for a group larger than 3 persons.

Teacher: Diego Castillo Franco, Ph.D.

Price: 1,899 PLN net (2,335.77 PLN including VAT).

Methods of payment: wire transfer.

Topics:

• Introduction to Amplicon Sequencing and Relevant Tools (Usearch, Vsearch, qiime2)
• Quality Assessment in Amplicon Sequencing Data
• Mapping and Read Counting Techniques for Amplicon Sequencing
• Pre-processing of Amplicon Counts
• Key Statistical Tests for Amplicon Sequencing Data
• Exploring Diversity Metrics and Taxonomic Assignments in Amplicon Sequencing
• Visualization of Amplicon Sequencing Results
• In-depth Case Study in Amplicon Sequencing Analysis

Learning Outcomes

By the end of the workshop, participants will:

1. Have experience working with various datasets and interpreting results effectively.
2. Be able to design their own workflows for data analysis.
3. Be capable of identifying and addressing data quality issues.
4. Apply different criteria to solve specific challenges in their research.
5. Gain hands-on experience in Amplicon Sequencing analysis, including:
1. Understanding its pros and cons,
2. Handling outputs from Second and Third Generation Sequencing technologies.
6. Enhance the accuracy, efficiency, and robustness of their research processes.
7. Be equipped to produce more reliable and impactful scientific findings through improved data analysis and interpretation skills.

Diego Castillo Franco, Ph.D.

Assistant professor at the Faculty of Biology, Gent University, Gent, Belgium. Experienced microbiologist and microbial ecologist with a strong background in bioinformatics (amplicon sequencing analysis, third-generation sequencing, metagenomics, metagenome assembled genomes). Research experience includes Antarctic microbiology, Amazon Rainforest, Hydropower reservoirs, the human microbiome, host-microbe interactions, genomic and metagenomic studies from prokaryotic communities, and metabolic inference analysis from different environments applying statistical approaches. Currently collaborates with Jagiellonian University (Krakow), University of Sao Paulo (Brazil), and Woods Hole Oceanographic Institution (USA).