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legal: adds a reference to the disclaimer
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claymcleod committed Nov 12, 2024
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Command line utility for working with next-generation sequencing files.
Command line utility for working with next-generation sequencing files.
<br />
<a href="https://github.com/stjude-rust-labs/ngs/wiki"><strong>Explore the docs »</strong></a>
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## 🎨 Features

* **[`ngs convert`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-convert).** Convert between next-generation sequencing formats.
* **[`ngs derive`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-derive).** Forensic analysis tool for next-generation sequencing data.
* **[`ngs generate`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-generate).** Generates a BAM file from a given reference genome.
* **[`ngs index`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-index).** Generates the index file to various next-generation sequencing files.
* **[`ngs list`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-list).** Utility to list various supported items in this command line tool.
* **[`ngs plot`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-plot).** Produces plots for data generated by `ngs qc`.
* **[`ngs qc`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-qc).** Generates quality control metrics for BAM files.
* **[`ngs view`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-view).** Views various next-generation sequencing files, sometimes with a query region.

- **[`ngs convert`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-convert).** Convert between next-generation sequencing formats.
- **[`ngs derive`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-derive).** Forensic analysis tool for next-generation sequencing data.
- **[`ngs generate`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-generate).** Generates a BAM file from a given reference genome.
- **[`ngs index`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-index).** Generates the index file to various next-generation sequencing files.
- **[`ngs list`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-list).** Utility to list various supported items in this command line tool.
- **[`ngs plot`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-plot).** Produces plots for data generated by `ngs qc`.
- **[`ngs qc`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-qc).** Generates quality control metrics for BAM files.
- **[`ngs view`](https://github.com/stjude-rust-labs/ngs/wiki/ngs-view).** Views various next-generation sequencing files, sometimes with a query region.

## 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.
- **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

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## 📝 License

* All code related to the `ngs derive instrument` subcommand is licensed under the [AGPL v2.0][agpl-v2]. This is not due to any strict requirement, but out of deference to some [code][10x-inspiration] that inspired our strategy (and from which patterns were copied), the decision was made to license this code consistently.
* The rest of this project is licensed as either [Apache 2.0][license-apache] or
[MIT][license-mit] at your discretion.
- All code related to the `ngs derive instrument` subcommand is licensed under the [AGPL v2.0][agpl-v2]. This is not due to any strict requirement, but out of deference to some [code][10x-inspiration] that inspired our strategy (and from which patterns were copied), the decision was made to license this code consistently.
- The rest of this project is licensed as either [Apache 2.0][license-apache] or
[MIT][license-mit] at your discretion.

Additionally, please see [the
disclaimer](https://github.com/stjude-rust-labs#disclaimer) that applies to all
crates and command line tools made available by St. Jude Rust Labs.

Copyright © 2021-Present [St. Jude Children's Research
Hospital](https://github.com/stjude).
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