Galaxy is an open source, web-based platform for accessible, reproducible, transparent computational and data intensive biomedical research. If you are new to Galaxy start here or consult the help resources within Galaxy.
- Accessible: programming experience is not required to easily upload data, run complex tools and workflows, and visualize results.
- Reproducible: Galaxy captures information so that you don't have to; any user can repeat and understand a complete computational analysis, from tool parameters to the dependency tree.
- Transparent: Users share and publish their histories, workflows, and visualisations via the web.
- Community centered: Our inclusive and diverse users (developers, educators, researchers, clinicians, etc.) are empowered to share their findings.
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.