Tools & Services

COVID-HUB-PL provides access to advanced digital laboratories comprising of tools and workflows for genomic, proteomic and structural data analysis, simulation and visualization


Genome visualization

Mapa genomiczna epidemiologii wirusa

The presented phylogenesis illustrates the evolutionary relationships between individual SARS-CoV-2 isolates during the ongoing COVID-19 pandemic, with particular emphasis on the area of Poland. Our goal is to analyze as many SARS-CoV-2 genomes as possible from people infected in Poland. The map also presents the genomic sequences of the virus from other European countries, and to a lesser extent from other regions of the world, to provide a more complete phylogenetic context. This context is important for understanding how different outbreaks of infection relate to each other and how the virus spreads around the globe.
We emphasize that a direct link between samples seen in a phylogenetic tree does not necessarily imply a direct epidemiological link between them. The sampling and testing of the coronavirus genomes are incomplete and heterogeneous, with new mutations appearing approximately every 2 weeks. For these reasons, prolonged periods in which no new mutations have been identified are not uncommon, making it difficult to infer a direct relationship between infections or the direction of virus transmission solely from the collected phylogenetic information.


Genomic data analysis

Workflows for NGS data analysis

Open source software developed by the ARCTIC network to facilitate the analysis and visualization of SARS-CoV-2 genomic data.

Toolkit used for bioinformatic analysis of SARS-CoV-2 data from Illumina.

Toolkit used for bioinformatic analysis of SARS-CoV-2 data from Oxford Nanopore.

Bioinformatics protocol for transferring the output from the Oxford Nanopore sequencing protocol to genome consensus sequences.

A tool that identifies differences between the collected sequences and the reference sequence used by Nextstrain. Nextclate reports potential data sequence quality issues.

An app that allows SARS-COV-2 (hCoV-19) data to be transferred directly to GISAID, providing real-time selection and annotation before the EpiCoV database is available to the public.


Other tools

COVID-19 diagnostic support

Tools for automatic analysis of medical imaging data using artificial intelligence.

Modeling of SARS-CoV-2 spread

Tools for visualization and modeling of the viral spread in the air in open and closed spaces.

Other services

ICT tools providing researchers and clinicians in the country with access to the resources of COVID-HUB-PL Platform.


  • trRosetta - AI tool for automated prediction of protein 3D structure
  • RNAstructure, RNAfold - tools for RNA and DNA 2D structure prediction and analysis
  • RNAComposer - a fully automated RNA 3D structure modeling server