ngs

Command line utility for working with next-generation sequencing files.
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🎨 Features

• ngs derive. Forensic analysis tool for next-generation sequencing data.
• ngs generate. Generates a BAM file from a given reference genome.
• ngs index. Generates the index file to various next-generation sequencing files.
• ngs list. Utility to list various supported items in this command line tool.
• ngs plot. Produces plots for data generated by ngs qc.
• ngs qc. Generates quality control metrics for BAM files.

Guiding Principles

• Modern, reliable foundation for everyday bioinformatics analysis—written in Rust. ngs aims to package together a fairly comprehensive set of analysis tools and utilities for everyday work in bioinformatics. It is built with modern, multi-core systems in mind and written in Rust. Though we are not there today, we plan to work towards this goal in the future.
• Runs on readily available hardware/software. We aim for every subcommand within ngs to run within most computing environments without the need for special hardware or software. Practically, this means we've designed ngs to run in any UNIX-like environment that has at least four (4) cores and sixteen (16) GB of RAM. Often, tools will run with fewer resources. This design decision is important and sometimes means that ngs runs slower than it otherwise could.

📚 Getting Started

Installation

To install the latest released version, you can simply use cargo.

bash cargo install ngs

To install the latest version on main, you can use the following command.

bash cargo install --locked --git https://github.com/stjude-rust-labs/ngs.git

🖥️ Development

To bootstrap a development environment, please use the following commands.

```bash

Clone the repository

git clone git@github.com:stjude-rust-labs/ngs.git cd ngs

Run the command line tool using cargo.

cargo run -- -h ```

🚧️ Tests

```bash

Run the project's tests.

cargo test

Ensure the project doesn't have any linting warnings.

cargo clippy

Ensure the project passes cargo fmt.

cargo fmt --check ```

Minimum Supported Rust Version (MSRV)

The minimum supported Rust version for this project is 1.64.0.

🤝 Contributing

Contributions, issues and feature requests are welcome! Feel free to check issues page.

📝 License

Copyright © 2021-Present St. Jude Children's Research Hospital.

This project is licensed as either Apache 2.0 or MIT at your discretion.