Researchers from the University of Helsinki have developed a novel bioinformatics pipeline called Lazypipe for identifying viruses in host-associated or environmental samples.
The pipeline was developed in close collaboration between virologists and bioinformaticians. The researchers believe they have succeeded to address many challenges typically encountered in viral metagenomics.
Previously, the
“These examples demonstrate the efficacy of Lazypipe data analysis for NGS libraries with very different DNA/RNA backgrounds, ranging from mammalian tissues to pooled and crushed arthropods,” says Dr.
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“The detection of SARS-CoV-2 without reference genome demonstrates the utility of Lazypipe for scenarios in which novel zoonotic viral agents emerge and can be quickly detected by NGS sequencing from clinical samples,” says Dr.
In early April, the research group tested libraries of SARS-CoV-2 positive samples with Lazypipe.
“We confirmed that the pipeline detected SARS-CoV-2 in 9 out of 10 libraries with default settings and without SARS-CoV-2 reference genome,” says Dr.
“Lazypipe could play a crucial role in prediction of emerging infectious diseases,” adds Assoc. Prof.
Reference: Plyusnin, I., Kant, R., Jääskeläinen, A.J., Sironen, T., Holm, L., Vapalahti, O. and Smura, T. Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types. Virus Evolution, 2020.
Lazypipe is available for the research community as a preinstalled module on
More information:
Ilja Pljusnin, Researcher, University of Helsinki
Tel. +358 2941 26480
Email:
Ravi Kant, Researcher, University of Helsinki
Tel. +358 2941 57054
Email:
Teemu Smura, Researcher, University of Helsinki
Tel. +358 2941 26480
Email:
Olli Vapalahti, Professor, University of Helsinki
Tel. +358 50 448 8842
Email: