Bots for SARS-CoV-2 genome surveillance
If you have to analyze a huge number of SARS-CoV-2 sequences on a regular basis, you will probably want to automate the execution of the analysis.
In particular, you may be looking for:
an automated way to upload newly available data into Galaxy and arrange it into collections
trigger execution of your variation analysis workflow, and proceed with downstream workflows for consensus building and reporting as soon as the variation workflow finishes
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 ...