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Welcome to Pipeliner - an open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Pipeliner provides access to a set of best-practices NGS pipelines developed, tested, and benchmarked by experts at CCBR and NCBR. This wiki is the main source of documentation for users and developers working with or contributing to Pipeliner. If you are unfamiliar with Pipeliner or this is the first time hearing about this project, please check out the links below.

Quick Navigation

Getting Started	Project & Community	FAQs	Pipeline Documentation
Introducing Pipeliner, prerequisites and how to get started	About our community, how to contribute and make feature requests	Frequently asked questions and solutions to common problems	Detailed technical documentation for users and developers about each of our pipelines

Questions or need help?

Please check out our FAQ or contact page for different ways of getting in touch with the team.

Getting started

1. Pre-requisites
2. How to launch the Pipeliner GUI

RNA-seq

I. Gene and isoform expression pipeline

1. Introduction
   1.1 Theory and practical guide to RNA-seq
   1.2 Supported Reference Genomes
   1.3 Tools and Versions
    1.3.1 Quantification and QC pipeline
    1.3.2 Differential Expression pipeline
2. Overview
   2.1 Quantification and QC pipeline
   2.2 Differential Expression pipeline
3. Tutorial
   3.1 Quantification and QC pipeline
4. TLDR
   4.1 Launch Pipeliner
   4.1 Run the Quantification and QC pipeline
5. References

II. Gene-fusions pipeline

1. Getting Started
2. Output from Quality-control
3. Output from Gene-fusions analysis
4. Additional Outputs

III. RNA variant calling pipeline

1. Getting Started
2. Outputs from Quality-control
3. Outputs from Variant Calling
4. Additional Outputs

ChIP-seq

I. Quality-control pipeline

1. Getting started with the Quality-control pipeline
2. About the Demo Dataset
3. Tutorial
   3.1 Step 0. Fill out the Project Information section
   3.2 Step 1. Setting Pipeline
   3.3 Step 2. Select Genome
   3.4 Step 3. Select your Data Directory
   3.5 Step 4. Select your Working Directory
   3.6 Step 5. Initialize your Working Directory
   3.7 Step 6. Set Peak information
   3.8 Step 7. Perform Dry Run
   3.9 Step 8. Run
4. Check progress
5. Confirm successful completion of Phase 1
6. Output files and directory structure
7. Tools and Versions
   7.1 Quality control assessment tools
   7.2 Data processing tools

II. Peak calling, differential peak calling, annotations, and motif pipeline

1. Phase 2: Peak calling, differential peak calling, annotations, and motif searches
   1.1 Step 1. Initial Setup
   1.2 Step 2. Select Pipeline Options
   1.3 Step 3. Set contrasts (Optional)
   1.4 Step 4. Perform Dry Run
   1.5 Step 5. Run
2. Check progress
3. Output files and directory structure

DNA-seq

I. Whole exome sequencing pipeline

1. Getting Started
2. Quality-control
3. Variant Detection Workflows
   3.1 Germline variant calling pipeline
   3.2 Tumor-Normal somatic variant calling pipeline
   3.3 Tumor-only somatic variant calling pipeline

II. Whole genome sequencing pipeline

1. Getting Started
2. Quality-control
3. Variant Detection Workflows
   3.1 Germline variant calling pipeline
   3.2 Tumor-Normal somatic variant calling pipeline
   3.3 Tumor-only somatic variant calling pipeline