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When you have DNA sequencing data, you often have to use bash / command line to glue together the various tooling. As an example: https://bedtools.readthedocs.
by joycian 7y ago
When you have DNA sequencing data, you often have to use bash / command line to glue together the various tooling.
As an example: https://bedtools.readthedocs.io/en/latest/ https://bedtools.readthedocs.io/en/latest/
- cure 7y agoYes, this is very common. But there are also many people who use Common Workflow Language (https://www.commonwl.org/ https://www.commonwl.org/) for this purpose. CWL allows for workflow portability between execution engines. The open source engine my team creates (Arvados - https://arvados.org https://arvados.org) is ideal for large-scale processing work. We store, process and manage petabytes of genome data with it, and execute workflows that span hundreds of simultaneous compute nodes.
- joycian 7y agoThis looks very cool! Thanks for sharing it. I'm definitely going to mention this in the next technical meeting at the research group.