The current COVID-19 pandemic represents a global threat. To help fight this pandemic, the NFDI4Microbiota consortium wants to make high-quality SARS-CoV-2 genome sequence data and metadata openly available according to the FAIR principles. To achieve this, NFDI4Microbiota offers help with sample preparation, genome sequencing and assembly, and data deposition.
If you would like to use this service contact us: contact-covid19-seq@ndfi4microbiota.de
Please note the following requirements when using these NFDI4Microbiota services:
- An order sheet with metadata (available soon) has to be filled in.
- NFDI4Microbiota will immediately deposit the sequenced genomes and underlying sequencing reads under a Creative Common 0 license (i.e. public domain dedication) in a public repository such as the European Nucleotide Archive (ENA) or the Sequence Read Archive (SRA).
Sample preparation
NFDI4Microbiota has a growing number of partner laboratories across all Germany that can assist you with sample preparation to avoid sending viral samples via mail. Following are examples of RNA extraction protocols and sample preparation methods used by these laboratories:
- RNA extraction: KingFisher, QIAcube
- Sample preparation for sequencing: amplified cDNA
Shipment will be made according to the RKI recommendations.
If you wish to support this initiative by acting as a laboratory preparing or sequencing samples, please contact us at covid-19-seq@nfdi4microbiota.de.
Genome sequencing and assembly
NFDI4Microbiota members offer sequencing and assembly of the SARS-CoV-2 genomes at net costs. Following are the examples of sequencing protocols, sequencing technologies and analysis workflows used/developed by the NFDI4Microbiota members:
- Sequencing protocol: nCoV-2019 sequencing protocol
- Sequencing technologies: MiSeq, SMRT Sequencing, MinION, Sanger sequencing
- Analysis workflow: nCov related workflows
Data deposition
NFDI4Microbiota will deposit the sequenced genomes and underlying sequencing reads in commonly used public repositories such as ENA or SRA.
Ordering and price
To order sample preparation and/or genome sequencing, please send us a filled order sheet (available soon) at: email address available soon. The price will be below € 100/sample (details available soon).
Laboratories involved
European Virus Bionformatics Center (EVBC) and
Jena University Hospital (UKJ)
- Contact details:
- Dr. Oliwia Makarewicz – oliwia.makarewicz@med.uni-jena.de
- Prof. Dr. Manja Marz – manja@uni-jena.de
- Address: At Klinikum 1, 07747 Jena, Germany
German Collection of Microorganisms and Cell Cultures GmbH (DSMZ)
- Contact details: Prof. Dr. Jörg Overmann – joerg.overmann@dsmz.de
- Address: Leibniz-Institute DSMZ, Inhoffenstr. 7B, 38124 Braunschweig, Germany
German Research Centre for Geosciences (GFZ)
- Contact details: Dr. Alexander Bartholomäus – abartho@gfz-potsdam.de
- Address: Telegrafenberg, 14473 Potsdam, Germany
Helmholtz Centre for Environmental Research (UFZ)
- Contact details:
- Dr. Ulisses Nunes da Rocha – ulisses.rocha@ufz.de
- Dr. René Kallies – rene.kallies@ufz.de
- Address: Permoserstrasse 15, 04318 Leipzig, Germany
Justus Liebig University Giessen (JLU Giessen)
- Contact details: Prof. Dr. John Ziebuhr – john.ziebuhr@viro.med.uni-giessen.de
- Address: Schubertstraße 81, 35392 Giessen, Germany
University Hospital of Düsseldorf (UKD)
- Contact details:
- Dr. Alexander Dilthey – alexander.dilthey@med.uni-duesseldorf.de
- Dr. Andreas Walker – andreas.walker@med.uni-duesseldorf.de
- Address: Moorenstrasse 5, 40225 Düsseldorf, Germany
Worm~Lab, University of Cologne (Uni Koeln)
- Contact details: Dr. Philipp Schiffer – a200302@uni-koeln.de
- Address: Zülpicher Straße 47b, 50674 Köln, Germany