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Welcome to sequence_handling!

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

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.

To run sequence_handling, go into the sequence handling directory and run:

./sequence_handling

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