The sample processing workflow for next generation sequencing from COMPARE partner Friedrich-Loeffler-Institut has been published.
The collection of COMPARE protocols for sample processing and sequencing is now being released.
‘A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection’ has been published online in Scientific Reports on 30 August 2018, DOI: 10.1038/s41598-018-31496-1.
The modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples is presented. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. The performance of the approach was confirmed using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.
The process of collecting and reviewing the various protocols from the COMPARE partners started early on in the project.
The protocols provided are Standard Operating Procedures (SOPs). SOPs are protocols that have been validated in detail and are already published. In some cases, different matrices and different pathogens (such as virus, bacteria, and/or parasite) have been used for validation.