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Welcome to sequence_handling!

This repository contains scripts that can automate the process of taking raw FastQ files through trimming, read mapping, and deduplication steps to create finished BAM files.

There are three kinds of scripts that are contained within this repository: Shell Scripts, Batch Submission Scripts, and Helper Scripts. These three kinds of scripts are used in very different ways.

To get set up with sequence_handling, open a terminal and type:

git clone https://github.com/MorrellLab/sequence_handling.git

or go to the repository on GitHub and select Download ZIP on the right-hand side. No GitHub account is required for downloading through either method.

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