QIAGEN Digital Insights resources for SARS-CoV-2 and COVID-19 genomic surveillance, research and analysis
QIAGEN CLC Genomics Workbench bioinformatics software is used by hundreds of microbiology and virology labs around the world for basic research and infectious disease epidemiology. QIAGEN CLC Genomics has also been critical for many labs on the front lines of the COVID-19 pandemic involved in sequencing the SARS-CoV-2 virus.
Two workflows are available for analyzing SARS-CoV-2 data. One workflow is customized for use with Ion AmpliSeq SARS-CoV-2 Research Panel data and the other is customized for use with QIAseq SARS-CoV-2 Primer Panel data. Both workflows can take one or multiple samples as input, which allows for analysis of either a single sample or comparison of multiple samples, based on a single workflow run.
The general approach of both workflows involves mapping the reads to a reference, generating a consensus sequence from the mapping, calling variants and generating outputs that allow for efficient review of results, including cross-sample comparison.
A detailed description is found in the manual.
The workflows are available in the workbench by installing the Biomedical Genomics Analysis plugin.
The workflow outputs can be used with the tools in QIAGEN CLC Microbial Genomics Module. Examples include:
For further details, see the sections in the manual on taxonomic analysis, functional analysis, phylogenetic trees using SNPs and k-mers, and large MLST scheme tools.
QIAGEN Ingenuity Pathway Analysis (IPA) is used by thousands of researchers and virology labs worldwide and cited extensively in studies of the host response to viruses. This valuable tool accelerates the understanding of ‘omics data from organisms and viruses to help assess interactions between the two, and reveal where therapeutics could potentially come into play to help modulate host response.
Read our brochure about IPA for viral research.
Check out our Coronavirus Network Explorer, available at no cost. Our data scientists have expanded upon recent peer-reviewed research to generate relevant SARS-CoV-2 protein networks using the QIAGEN Knowledge Base as well as artificial intelligence. This freely available tool helps you visualize how SARS-CoV-2 proteins interact with human host proteins to disable protective responses and pathways, and explore hypotheses around how to fight coronavirus. The Coronavirus Network Explorer supports and accelerates your research by helping you gain a deeper understanding of how SARS-CoV-2 affects the host and behaves biologically.
Accelerate your antiviral host response research with QIAGEN Viral Land, a gene expression database on viral studies delivered in a simple-to-use web portal known as QIAGEN OmicSoft Land Explorer. Viral land is a highly curated and re-processed collection of high-value human viral host and viral vaccine RNA-seq and microarray expression data, harmonized into a single platform.
This specialized collection of viral ‘omics data is available through QIAGEN Discovery Bioinformatics Services.