If you have to analyze a huge number of SARS-CoV-2 sequences on a regular basis, you will probably want to automate the excution of the analysis.
In particular, you may be looking for:
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an automated way to upload newly available data into Galaxy and arrange it into collections
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trigger execution of your variation analysis workflow, and proceed with downstream workflows for consensus building and reporting as soon as the variation workflow finishes
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arrange the workflow results into batch-specific histories
Here you find the solution used by usegalaxy.* instances to track National Genome Surveillance projects, like COG-UK, and reanalyze their data as it becomes publicly available.
Our automation scripts can be combined with any scheduling system and allow us to achieve a daily throughput of more than 1,000 samples on any individual usegalaxy.* instance with minimal impact on the analysis needs of our users.
You can use these scripts with little or no modifications to automate your own SARS-CoV-2 analyses on a public server or your own instance of Galaxy.
Interested? Then read on ...