{"id":15444425,"url":"https://github.com/jlsteenwyk/biokit","last_synced_at":"2026-03-13T04:33:52.356Z","repository":{"id":38305210,"uuid":"392781797","full_name":"JLSteenwyk/BioKIT","owner":"JLSteenwyk","description":"a versatile toolkit for processing and analyzing diverse types of sequence 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align=\"center\"\u003e\n  \u003ca href=\"https://github.com/jlsteenwyk/biokit\"\u003e\n    \u003cimg src=\"https://github.com/JLSteenwyk/BioKIT/blob/main/docs/_static/img/biokit_logo.jpg\" alt=\"Logo\" width=\"400\"\u003e\n  \u003c/a\u003e\n  \u003cp align=\"center\"\u003e\n    \u003ca href=\"https://jlsteenwyk.com/BioKIT/\"\u003eDocs\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/biokit/issues\"\u003eReport Bug\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/biokit/issues\"\u003eRequest Feature\u003c/a\u003e\n  \u003c/p\u003e\n    \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://github.com/JLSteenwyk/BioKIT/actions\" alt=\"Build\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JLSteenwyk/BioKIT/ci.yml?branch=main\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://codecov.io/gh/JLSteenwyk/BioKIT\" alt=\"Coverage\"\u003e\n          \u003cimg src=\"https://codecov.io/gh/JLSteenwyk/BioKIT/branch/main/graph/badge.svg?token=5X9C6YAVIG\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://github.com/jlsteenwyk/biokit/graphs/contributors\" alt=\"Contributors\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/contributors/jlsteenwyk/biokit\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://bsky.app/profile/jlsteenwyk.bsky.social\" target=\"_blank\" rel=\"noopener noreferrer\"\u003e\n          \u003cimg src=\"https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky\u0026logoColor=fff\"\u003e\n        \u003c/a\u003e\n        \u003cbr /\u003e\n        \u003ca href=\"https://pepy.tech/badge/jlsteenwyk-biokit\"\u003e\n          \u003cimg src=\"https://static.pepy.tech/personalized-badge/jlsteenwyk-biokit?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=PyPi%20Downloads\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://lbesson.mit-license.org/\" alt=\"License\"\u003e\n            \u003cimg src=\"https://img.shields.io/badge/License-MIT-blue.svg\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://pypi.org/project/jlsteenwyk-biokit/\" alt=\"PyPI - Python Version\"\u003e\n            \u003cimg src=\"https://img.shields.io/pypi/pyversions/jlsteenwyk-biokit\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac079/6583183?login=true\"\u003e\n          \u003cimg src=\"https://zenodo.org/badge/DOI/10.1093/genetics/iyac079.svg\"\u003e\n        \u003c/a\u003e\n    \u003c/p\u003e\n\u003c/p\u003e\n\nBioKIT is a UNIX shell toolkit for processing molecular sequence data.\u003cbr /\u003e\u003cbr /\u003e\nIf you found BioKIT useful, please cite the following: *BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data*. Genetics. doi: [10.1093/genetics/iyac079](https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac079/6583183).\n\u003cbr /\u003e\u003cbr /\u003e\n\n---\n\nThis documentation covers downloading and installing BioKIT. Details about each function as well as tutorials for using BioKIT are available in the \u003ca href=\"https://jlsteenwyk.com/BioKIT/\"\u003eonline documentation\u003c/a\u003e.\n\n\u003cbr /\u003e\n\n**Installation** \u003cbr /\u003e\n\n**If you are having trouble installing BioKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**\n\nTo install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:\n```shell\n# create virtual environment\npython -m venv .venv\n# activate virtual environment\nsource .venv/bin/activate\n# install biokit\npip install jlsteenwyk-biokit\n```\n\n**Note, the virtual environment must be activated to use biokit.**\n\nAfter using biokit, you may wish to deactivate your virtual environment and can do so using the following command:\n```shell\n# deactivate virtual environment\ndeactivate\n```\n\n\u003cbr /\u003e\n\nSimilarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:\n```shell\n# download\ngit clone https://github.com/JLSteenwyk/BioKIT.git\ncd BioKIT/\n# create virtual environment\npython -m venv .venv\n# activate virtual environment\nsource .venv/bin/activate\n# install\nmake install\n```\nTo deactivate your virtual environment, use the following command:\n```shell\n# deactivate virtual environment\ndeactivate\n```\n**Note, the virtual environment must be activated to use biokit.**\n\n\u003cbr /\u003e\n\nTo install via anaconda, execute the following command:\n```shell\nconda install -c jlsteenwyk jlsteenwyk-biokit\n```\nVisit here for more information:\nhttps://anaconda.org/JLSteenwyk/jlsteenwyk-biokit\n\n\u003cbr /\u003e\n\nTo test biokit installation, launch the help message\n\n```shell\nbiokit -h\n```\n\n## Development\n\nCommon local quality checks and profiling workflows are documented in:\n\n- `docs/dev/developer_workflow.rst`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fbiokit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjlsteenwyk%2Fbiokit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fbiokit/lists"}