https://github.com/hail-is/hail

Cloud-native genomic dataframes and batch computing
https://github.com/hail-is/hail

bioinformatics genetics genomics gwas hail python software vcf

Last synced: about 2 months ago
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Cloud-native genomic dataframes and batch computing

• Host: GitHub
• URL: https://github.com/hail-is/hail
• Owner: hail-is
• License: mit
• Created: 2015-10-27T20:55:42.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2024-03-15T20:44:05.000Z (3 months ago)
• Last Synced: 2024-03-18T04:00:51.011Z (3 months ago)
• Topics: bioinformatics, genetics, genomics, gwas, hail, python, software, vcf
• Language: Python
• Homepage: https://hail.is
• Size: 118 MB
• Stars: 925
• Watchers: 56
• Forks: 235
• Open Issues: 223
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff
  • Authors: AUTHORS

Lists

• Awesome-Bioinformatics - Hail - Scalable genomic analysis. (Next Generation Sequencing / Data Analysis)
• awesome-spark - Hail - commit/hail-is/hail.svg"> - Genetic analysis framework. (Packages / Bioinformatics)
• awesome-python-machine-learning-resources - GitHub - 0% open · ⏱️ 26.08.2022): (医疗领域)
• awesome-stars - hail-is/hail - Cloud-native genomic dataframes and batch computing (Python)
• awesome-spark - Hail - commit/hail-is/hail.svg"> - Genetic analysis framework. (Packages / Bioinformatics)
• Awesome-Bioinformatics-CN - Hail - 可扩展基因组分析(类似pandas？) (二代测序 / 数据分析)
• top-life-sciences - **hail-is/hail** - native genomic dataframes and batch computing<br>`bioinformatics`, `genetics`, `genomics`, `gwas`, `hail`, `python`, `software`, `vcf`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 946 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 238 <img src='https://github.com/HubTou/topgh/blob/main/icons/watchers.png'> 55 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Python <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> MIT license <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-06-05 17:48:05 | (Ranked by starred repositories)

README

        
# Hail

[![Zulip](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://hail.zulipchat.com?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [![DOI](https://zenodo.org/badge/45069467.svg)](https://zenodo.org/badge/latestdoi/45069467) [![PyPI version](https://badge.fury.io/py/hail.svg)](https://badge.fury.io/py/hail)

[Hail](https://hail.is) is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.

Hail is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS).

Hail is exposed as a Python library, using primitives for distributed queries and linear algebra implemented in Scala, [Spark](https://spark.apache.org/docs/latest/index.html), and increasingly C++.

See the [documentation](https://hail.is/docs/0.2/) for more info on using Hail.

### Community

Hail has been widely adopted in academia and industry, including as the analysis platform for the [genome aggregation database](https://gnomad.broadinstitute.org) and [UK Biobank rapid GWAS](https://www.nealelab.is/uk-biobank). Learn more about [Hail-powered science](https://hail.is/references.html).

### Contribute

If you'd like to discuss or contribute to the development of methods or infrastructure, please:

- see the [For Software Developers](https://hail.is/docs/0.2/getting_started_developing.html) section of the installation guide for info on compiling Hail

- chat with us about development in our [Zulip chatroom](https://hail.zulipchat.com)

- visit the [Development Forum](https://dev.hail.is) for longer-form discussions

Hail uses a continuous deployment approach to software development, which means we frequently add new features. We update users about changes to Hail via the [Discussion Forum](https://discuss.hail.is). We recommend creating an account on the Discussion Forum so that you can subscribe to these updates as well.

### Maintainer

Hail is maintained by a team in the [Neale lab](https://nealelab.is/) at the [Stanley Center for Psychiatric Research](https://www.broadinstitute.org/stanley) of the [Broad Institute of MIT and Harvard](https://www.broadinstitute.org) and the [Analytic and Translational Genetics Unit](https://www.atgu.mgh.harvard.edu/) of [Massachusetts General Hospital](https://www.massgeneral.org/).

Contact the Hail team at [email protected].

### Citing Hail

If you use Hail for published work, please cite the software. You can get a

citation for the version of Hail you installed by executing:

```python

import hail as hl

print(hl.citation())

```

Which will look like:

```

Hail Team. Hail 0.2.13-81ab564db2b4. https://github.com/hail-is/hail/releases/tag/0.2.13.

```

##### Acknowledgements

The Hail team has several sources of funding at the Broad Institute:

- The Stanley Center for Psychiatric Research, which together with Neale Lab has provided an incredibly supportive and stimulating home.

- Principal Investigators Benjamin Neale and Daniel MacArthur, whose scientific leadership has been essential for solving the right problems.

- Jeremy Wertheimer, whose strategic advice and generous philanthropy have been essential for growing the impact of Hail.

We are grateful for generous support from:

- The National Institute of Diabetes and Digestive and Kidney Diseases

- The National Institute of Mental Health

- The National Human Genome Research Institute

- The Chan Zuckerberg Initiative

We would like to thank Zulip for supporting

open-source by providing free hosting, and YourKit, LLC for generously providing

free licenses for YourKit Java

Profiler for open-source development.