Using Omics Pipe — Omics Pipe v1.1.3 Documentation

Omics Pipe is a Python framework for automating ‘best practice’ next generation sequencing pipelines. Omics Pipe can be run from the command-line by providing it with a YAML parameter file specifying your directory structure and software specific parameters. This executes a parallel automated pipeline on a Distributed Resource Management system (local cluster or Amazon Web Services (AWS)) that efficiently handles job resource allocation, monitoring and restarting. The goals of Omics Pipe are to provide researchers with an open-source computational solution to implement ‘best practice’ pipelines with minimal development overhead and providing visual outputs to aid the researcher.