Amplicon sequencing analysis (2-days online workshop)

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: October 21 and 22, 2024, 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: 380 EUR/USD (plus VAT if applicable).


  • 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

Diego Castillo Franco, Ph.D.

Works at Institute of Zoology of Jagiellonian University, Krakow. 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 Ghent University (Belgium), University of Sao Paulo (Brazil), and Woods Hole Oceanographic Institution (USA).



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