Pre-Congress Workshop
PASTA: Best Practices in Deep Amplicon Sequencing for Parasitology
Introduction
Deep amplicon sequencing is transforming parasitology by enabling high‑throughput profiling of complex parasite communities and detection of resistance‑associated genetic variants from mixed samples. It integrates metabarcoding and targeted sequencing approaches to identify species and quantify genetic variation, often independent of parasite life stage.
Despite its power, successful application requires careful attention to study design, marker choice, data processing, and reproducibility. As outlined in the “Ten simple rules” (1), robust implementation depends on integrating molecular workflows with traditional parasitology and transparent reporting practices.
The workshop follows a structured PASTA framework (Parasitology Amplicon Sequencing and Transparent Analysis), guiding participants from raw sequence data to robust and interpretable ASV tables.
Workshop Overview
This half‑day, hands‑on pre‑congress workshop introduces deep amplicon sequencing analysis in the context of parasitology and parasite identification.
Participants will work with provided sample datasets and follow a complete, guided workflow from raw FASTQ files to interpretable amplicon sequence variant (ASV) tables using the DADA2 pipeline. The workshop emphasises practical implementation aligned with best‑practice principles, including data curation, distinguishing biological signal from technical noise and transparent reporting.
This workshop serves as an accessible primer for participants new to deep amplicon sequencing, while also providing practical guidance aligned with current best practices. Structured scripts and guided checkpoints will support participants throughout, enabling them to reproduce the analysis workflow independently after the session.
No specialised bioinformatics knowledge is required. Participants should have a basic understanding of Excel, familiarity with the Windows environment and the ability to navigate folder structures.
Participation is limited to twelve attendees to ensure an interactive and supportive learning environment.
What the workshop covers
Introduction to deep amplicon sequencing, metabarcoding and targeted amplicon applications in parasitology
Understanding FASTQ data and sequencing outputs
Guided analysis using the DADA2 pipeline in RStudio
Quality filtering, trimming, denoising, read merging and chimera removal
Generating and interpreting ASV tables while distinguishing biological signals from technical noise
Linking results to parasitological interpretation with reproducible and transparent reporting practices
Learning Outcomes
Explain the principles and applications of deep amplicon sequencing in parasitology.
Describe the key steps in a standard, reproducible metabarcoding workflow.
Apply the DADA2 pipeline to process raw sequencing data from FASTQ files into ASVs.
Interpret ASV outputs by distinguishing biological signal from technical noise.
Implement good practices in the transparent and reproducible reporting of amplicon data.