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Services: genomics & transcriptomics

Analysis of SARS-CoV-2 data using GALAXY

The ELIXIR Greece Galaxy instance contains among others (e.g. aligners, Quality Control, data type conversion, filtering etc) the best practices for the analysis of SARS-CoV-2 data according to and the corresponding pipelines. More specifically, regarding SARS-CoV-2 you can find the following:

  • Pre-processing of raw read data
  • Assembly of SARS-CoV-2 genome
  • Estimation of timing for most recent common ancestor (MRCA)
  • Analysis of variation within individual isolates
  • Analysis of Spike protein substitutions
  • Analysis of recombination and selection
  • Screening of the main protease (Cheminformatics)

The link to the server is and currently anyone can register and use. The users’ jobs are executed on a cluster of 48 CPUs, 192 GB RAM and 3 TB of storage. Depending on user needs, more resources (CPU, RAM, storage) and tools can be installed.