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Introduction 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 set up 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 see usage information about sequence_handling, go into the sequence handling directory

cd sequence_handling

and run:

./sequence_handling

Next: Useful Information