Whole Genome Sequencing

Application of whole genome sequencing (WGS) offers the possibility to rapidly transform and improve our understanding of the epidemiology of antimicrobial resistance (AMR) determinants. Below you find links to training material and publications, as well as more practical guidance and tools for performing WGS.

Please see further details in relation to below:

How to get started

When starting up whole genome sequencing, several considerations are necessary about DNA extraction, library preparation, sequencing and data processing.

Protocol and quality assessment

Suggestions for commonly used technologies and methods within these areas are covered in the protocol below.

Tools and software

Tools and software that can be used for processing whole genome sequencing data.

Benchmarking

Benchmarking exercises are important to assess the performance, and reliability of the available bioinformatics tools which have different complexity in design and function.

Inter-EURLs Working Group on NGS

The Inter-European Union Reference Laboratories (EURLs) Working Group (WG) has been established by the European Commission to promote the use of Next Generation Sequencing (NGS).

Upload to ENA

The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information.

E-learning

Link to e-learning courses on Antimicrobial Resistance, Whole Genome Sequencing and Metagenomics.

Proficiency test

It is advisable for laboratories to participate in proficiency tests (PT) regarding WGS. Find further details about an example of a relevant PT here.

Companies for outsourcing

If performing whole genome sequencing is not possible in your laboratory facilities, there are several companies available world-wide to whom some or all of the sequencing and bioinformatics tasks can be outsourced.

Recommended publications

Please find information on recommended publications here.

Useful links

Find more information on WGS and AMR surveillance here.