Deliverables

The following is a list of Deliverables for the COMPARE project. Deliverables that have been approved by the European Commission and are for public dissemination will be made available here.

Deliverable no.	Title	Dissemination
D1.1	Automated tools for rapid assessment of key transmission parameters	Public
D1.2	Risk based surveillance plans, sampling algorithms and protocols	Public
D1.3	Generic RA framework	Public
D2.1	Matrix-dependent sample handling protocols	Public
D2.2	Standard protocol sample processing	Public
D2.3	Sequencing workflow	Public
D2.4	Data analysis pipeline	Public
D2.5	Testing results of molecular analytical workflow in ring trials	Confidential
D2.6	Testing results of molecular analytical workflow in ring trials	Confidential
D2.7	Testing results of molecular analytical workflow in ring trials	Confidential
D3.1	Analytical workflow for clinical diagnostic application	Public
D3.2	Prediction algorithm AMR markers	Public
D3.3	Standardized protocols	Public
D4.1	Reference sequence database	Confidential
D4.2	Algorithm for detection of informative (sub)types	Public
D4.3	Analytical workflow	Public
D4.4	Validated RA model for NGS data	Public
D5.1	Update of pathogen repositories	Confidential
D5.2	Tools for rapid sequence based detection of strain specific clusters	Public
D5.3	Phylogenetic and phylogeographic tools	Public
D5.4	Tools for detecting SNPs	Public
D5.5	Methods for prediction of pathogen phenotype from genotype	Public
D6.1	Report on NGS based diagnostics in comparison to gold standard methods	Public
D6.2	Report on WGS and NGS based detection of AMR in stool samples in patients and travelers	Confidential
D6.3	Reports on WGS and NGS based hospital outbreak detection and monitoring	Confidential
D7.1	Database of reference genomes	Confidential
D7.2	Report for cluster detection for all pilot organisms	Confidential
D7.3	Database of markers for host-association and ecophysiology	Confidential
D7.4	Improved guidelines for interpretation criteria for defining clusters of disease	Confidential
D8.1	Report on results of pilot study of metagenomic pathogen detection	Confidential
D8.2	NGS sequencing data	Confidential
D8.3	Identification of key drivers of evolution	Confidential
D9.1	Hardware and cloud environment	Confidential
D9.2	Registry and data resource component	Confidential
D9.3	Generic workflow engine	Public
D9.4	Integrated analytical workflows	Public
D9.5	Full technical specifications	Public
D9.6	Integration with map / tree / network visualisation components to the COMPARE data portal	Confidetial
D10.1	Stakeholder Analysis Report	Confidential
D10.2	Targeted Message Report	Confidential
D10.3	Initial version COMPARE RCT box V1	Public
D10.4	Beta version COMPARE RCT box V2	Public
D11.1	EAP report 1st cycle	Confidential
D11.2	EAP report 2nd cycle	Confidential
D11.3	EAP report 3rd cycle	Confidential
D11.4	EAP report 4th cycle	Confidential
D11.5	EAP report 5th cycle	Confidential
D12.1	Report legal limitations, conditions and obligations	Confidential
D12.2	Ethical framework and charter	Confidential
D12.3	Report data-sharing guidelines	Confidential
D13.1	Contact database	Confidential
D13.2	Leaflet and templates	Public
D13.3	Public website	Public
D13.4	E-learning materials	Public
D13.5	Workshop programme	Public
D13.6	Publications and presentations	Public
D14.1	CE Framework	Public
D14.2	Methodologies report	Public
D14.3	Paper on methodology and results of estimating the value of safety	Public
D14.4	Case study cost- effectiveness report	Public
D14.5	Cost-effectiveness report	Public
D15.1	Project Management manual	Confidential
D15.2	Internal reporting templates	Confidential
D15.3	Plan for the Dissemination and Exploitation of Results	Confidential

Updated by Jeffrey Edward Skiby on 7 September 2020

Contact

Jeffrey Edward Skiby

Senior Academic Officer

DTU National Food Institute

+45 35 88 66 04
jeesk@food.dtu.dk

Updated by Jeffrey Edward Skiby on 7 September 2020