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Getting Started

This repository contains scripts, called 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

If you don't have Git installed, you can 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

Parallel Processing

This repository has a heavy dependency on GNU Parallel; most of the handlers use GNU Parallel to speed the processing of multiple samples. While this speeds processing, be aware that: standard laptops, tablets, and desktop computers may not be appropriate. The handlers in the repository are most appropriate for use on supercomputers; this repository was designed with the Minnesota Supercomputing Institute (MSI) in mind.

Running sequence_handling on MSI

MSI's resources make extensive use of a module system, in which software is installed and maintained by MSI and users can call upon modules as needed. These handlers are designed to call upon modules whenever possible, however some dependencies are not available through MSI. Please check the dependencies page to see which programs are necessary for which handlers.

If you are running these handlers on a system other than an MSI cluster, check your system for the presence of the above dependencies.

Next Steps

Take a look at the recommended workflow to familiarize yourself with the goals of this repository. To begin running the pipeline, you will need to:

1. Install or locate the correct version of each of the dependencies
2. Create a list of your raw samples using sample_list_generator.sh
3. Fill out a configuration file for your project