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PughLab pipeline suite

Installation and Dependencies

This is a collection of pipelines to be used for NGS (both DNA and RNA) analyses, from alignment to variant calling.

Start by creating a clone of the repository:

cd /path/to/some/directory
git clone git@github.com:pughlab/pipeline-suite.git

Additionally, the report generation portion of this tool requires installation of the BPG plotting package for R: https://CRAN.R-project.org/package=BoutrosLab.plotting.general

Overview

DNA Pipeline

RNA Pipeline

Table of contents

1. Input file format
2. Workflow (How to start a project)
3. DNA Pipeline
   1. Running individual tools
   2. Pipeline Output
   3. Using a panel of normals for filtering
4. RNA Pipeline
   1. Running individual tools
   2. Pipeline Output
5. Fragmentomics Pipeline
6. EM-Seq Pipeline
7. Tips for saving space
8. FAQ