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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: 4 days 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 (about 9 years ago)
- Default Branch: main
- Last Pushed: 2024-10-29T17:47:00.000Z (3 months ago)
- Last Synced: 2024-10-29T19:01:53.608Z (3 months ago)
- Topics: bioinformatics, genetics, genomics, gwas, hail, python, software, vcf
- Language: Python
- Homepage: https://hail.is
- Size: 124 MB
- Stars: 979
- Watchers: 56
- Forks: 246
- Open Issues: 254
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
- Authors: AUTHORS
Awesome Lists containing this project
- Awesome-Bioinformatics - Hail - Scalable genomic analysis. (Next Generation Sequencing / Data Analysis)
- 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)
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README
# Hail
[](https://hail.zulipchat.com?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [](https://zenodo.org/badge/latestdoi/45069467) [](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.
