Omics Pipe

Omics Pipe is an open-source, modular computational platform that automates best practice multi-omics data analysis 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 or on AWS. This executes a parallel automated pipeline on a Distributed Resource Management system 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 in biological interpretation. Currently Omics Pipe automates and provides summary reports for two RNA sequencing (RNA-seq) pipelines, variant calling from whole exome sequencing (WES) and whole genome sequencing (WGS) based on the Genome Analysis Toolkit (GATK), two ChIP-seq pipelines and a custom RNA-seq pipeline for personalized cancer genomic medicine reporting

Omics Pipe repository: https://bitbucket.org/sulab/omics_pipe

Omics Pipe Python Package: https://pypi.python.org/pypi/omics_pipe

• Documentation: https://pythonhosted.org/omics_pipe/