Workpackage 2

Harmonised standards for sample processing and sequencing

WP leader: Martin Beer, FLI (4)
co-leader: Simone Caccio, ISS (8)

Overall task: To develop harmonized analytical workflows for generation of high-quality NGS data in combination with relevant metadata for pathogen detection and typing across sample types, pathogens and domains.

1. To optimize and harmonize sample handling for NGS and related methods.

2. To develop standardized protocols for sample processing for different sample types and viruses, bacteria and parasites.

3. To develop standardized sequencing protocols for the different pathogens as well as for different purposes (surveillance, diagnostics, single isolates, metagenomics).

4. To improve sequence analyses, including novel bioinformatics tools for metagenomics, isolate typing, and de novo reference-less identification of pathogen-related sequences.

5. To develop sequence curation and storage protocols and tools.

6. To develop historic and prospective biobanks as reference.

7. To develop a scheme for ring trials and external quality assurance systems.


Martin Beer
Friedrich Loeffler Institut - Bundesforschungsinstitut Fuer


Simone Caccio
Instituto Superiore di Sanita
16 JULY 2024