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 https://covid19.galaxyproject.org 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 https://usegalaxy.elixir-greece.org 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.