Overview

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Omics Pipe - A computational framework for reproducible next generation sequencing analysis

Summary

Welcome to the documentation for Omics Pipe! Omics pipe is an open-source, modular computational platform that automates ‘best practice’ multi-omics data analysis pipelines published in Nature Protocols and other commonly used pipelines, such as GATK. It currently automates and provides summary reports for two RNA-seq pipelines, variant calling from whole exome sequencing (WES), variant calling and copy number variation analysis from whole genome sequencing (WGS), two ChIP-seq pipelines and a custom RNA-seq pipeline for personalized genomic medicine reporting. It also provides automated support for interacting with the The Cancer Genome Atlas (TCGA) datasets, including automatic download and processing of the samples in this database.

omics_pipe_overview.png

omics_pipe_pipelines_20140402.png

Requirements

HPC Cluster or AWS Star Cluster

Python 2.6 or newer

Software Dependencies installed as Modules

Reference Databases

Installation

Option 1

pip install omics_pipe

Option 2

easy_install omics_pipe

Option 3 -- download/extract the source code

python setup.py install

Option 4 -- install the latest code directly from the repository

pip install -e hg+https://bitbucket.org/sulab/omics_pipe#egg=omics_pipe

Option 5 -- if you do not have administrator privileges

*Step 1: Set up a [Python virtual environment](http://docs.python-guide.org/en/latest/dev/virtualenvs/)
*Step 2: Use one of the Options (1-4) above to install Omics Pipe within your virtual environment.

Usage

command-line usage::

omics_pipe [-h] [--custom_script_path CUSTOM_SCRIPT_PATH]
              [--custom_script_name CUSTOM_SCRIPT_NAME]
              [--compression {gzip,bzip}]
              {RNAseq_Tuxedo, RNAseq_count_based, RNAseq_cancer_report, RNAseq_TCGA, RNAseq_TCGA_counts, Tumorseq_MUTECT, miRNAseq_count_based, miRNAseq_tuxedo, WES_GATK, WGS_GATK, SomaticInDels, ChIPseq_MACS, ChIPseq_HOMER,  custom} 
              parameter_file

Documentation

Tutorial for omics_pipe

Website

Omics Pipe home page

Repository

Bitbucket Repo

Distribution

PyPI

bioRxiv Preprint

bioRxiv

AWS

Current DB Snapshot: snap-2db684e3 (27 Aug 2014)

Current AMI: ami-2b676b6e

Contact

Feedback welcome at: omics_pipe@googlegroups.com

Twitter: @kathleenfisch

Google Group: https://groups.google.com/forum/#!forum/omics_pipe