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Welcome to sequence_handling!

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

There are two kinds of scripts that are contained within this repository, with one exception: Shell Scripts and Batch Submission Scripts. These two kinds of scripts are run 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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