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Mitochondrial Genome Pipeline

Project description

Getting Started

This project can be downloaded through pip install mitopipeline to install the latest version of mitopipeline. Or, you can directly clone the repository through git clone https://github.com/timmykuo/mitopipeline.git, navigate to the cloned repository, and run python3 setup.py install. Documentation is hosted through readthedocs.

Users will have to download samtools and bwa, make them, and include the path to the executable in their $PATH variable or copy them to their bin folder so that they can be run from the command line. Download links for samtools and bwa. In addition, 3rd party software packages that they wish to use on their own (such as GATK, ANNOVAR, etc.) need to be downloaded before being able to use them in the pipeline.

Purpose

In genetics research, researchers often require raw genome data to be run on different softwares first to extract useful information such as variant information before it can be analyzed. Thus, we want to provide a pipeline that allows users to streamline their processing automatically for them.

The steps included within this pipeline include extracting mitochondrial genome from human genome, clipping, splitting the gap for Complete Genomics data, alignment into NuMT removals, and other software packages such as GATK, SNPEFF, ANNOVAR.

Pipeline

https://raw.githubusercontent.com/timmykuo/mitopipeline/master/doc/pipeline.png

The steps shown in this figure are described further in the Pipeline Steps page. Each step can be omitted if it’s unncessary for your pipeline.

Credits

The dependency management is controlled through a python package called Luigi. In addition, many of the steps in the pipeline were adapted from scripts written by Sneha Grandhi. Check out her Github, LinkedIn, or contact her through her email: sneha_grandhi@hms.harvard.edu.

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