{"id":23658975,"url":"https://github.com/biodatageeks/polars-bio","last_synced_at":"2025-07-29T10:09:00.632Z","repository":{"id":265979229,"uuid":"894611596","full_name":"biodatageeks/polars-bio","owner":"biodatageeks","description":"Blazing-Fast Bioinformatic Operations on Python DataFrames","archived":false,"fork":false,"pushed_at":"2025-07-18T14:03:31.000Z","size":9518,"stargazers_count":68,"open_issues_count":48,"forks_count":22,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-18T18:21:05.939Z","etag":null,"topics":["arrow","bioinformatics","dataframes","datafusion","genomic-intervals","genomic-ranges","genomics","pandas","polars","rust-lang"],"latest_commit_sha":null,"homepage":"http://biodatageeks.org/polars-bio/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biodatageeks.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-11-26T16:58:18.000Z","updated_at":"2025-07-17T11:24:12.000Z","dependencies_parsed_at":"2025-01-12T23:18:06.708Z","dependency_job_id":"5b29edda-31b5-480f-8f43-773c272034dd","html_url":"https://github.com/biodatageeks/polars-bio","commit_stats":null,"previous_names":["biodatageeks/polars-bio"],"tags_count":40,"template":false,"template_full_name":null,"purl":"pkg:github/biodatageeks/polars-bio","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biodatageeks%2Fpolars-bio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biodatageeks%2Fpolars-bio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biodatageeks%2Fpolars-bio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biodatageeks%2Fpolars-bio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biodatageeks","download_url":"https://codeload.github.com/biodatageeks/polars-bio/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biodatageeks%2Fpolars-bio/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267668689,"owners_count":24124966,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-29T02:00:12.549Z","response_time":2574,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["arrow","bioinformatics","dataframes","datafusion","genomic-intervals","genomic-ranges","genomics","pandas","polars","rust-lang"],"created_at":"2024-12-29T01:48:47.271Z","updated_at":"2025-07-29T10:09:00.624Z","avatar_url":"https://github.com/biodatageeks.png","language":"Python","funding_links":[],"categories":["Libraries/Packages/Scripts","Libraries","Next Generation Sequencing"],"sub_categories":["Polars plugins","Bioinformatics","Python Modules"],"readme":"# polars-bio - Next-gen Python DataFrame operations for genomics!\n![PyPI - Version](https://img.shields.io/pypi/v/polars-bio)\n![GitHub License](https://img.shields.io/github/license/biodatageeks/polars-bio)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/polars-bio)\n![GitHub commit activity](https://img.shields.io/github/commit-activity/m/biodatageeks/polars-bio)\n[![](https://dcbadge.limes.pink/api/server/https://discord.gg/bpxQ4Yxhk5?style=flat)](https://discord.gg/bpxQ4Yxhk5)\n\n![CI](https://github.com/biodatageeks/polars-bio/actions/workflows/publish_to_pypi.yml/badge.svg?branch=master)\n![Docs](https://github.com/biodatageeks/polars-bio/actions/workflows/publish_documentation.yml/badge.svg?branch=master)\n![logo](docs/assets/logo-large.png)\n\n\n\n\n[polars-bio](https://pypi.org/project/polars-bio/) is a Python library for genomics built on top of [polars](https://pola.rs/), [Apache Arrow](https://arrow.apache.org/) and [Apache DataFusion](https://datafusion.apache.org/).\nIt provides a DataFrame API for genomics data and is designed to be blazing fast, memory efficient and easy to use.\n\n## Key Features\n* optimized for [performance](https://biodatageeks.org/polars-bio/performance/) and memory [efficiency](https://biodatageeks.org/polars-bio/performance/#memory-characteristics) for large-scale genomics datasets analyses both when reading input data and performing operations\n* popular genomics [operations](https://biodatageeks.org/polars-bio/features/#genomic-ranges-operations) with a DataFrame API (both [Pandas](https://pandas.pydata.org/) and [polars](https://pola.rs/))\n* [SQL](https://biodatageeks.org/polars-bio/features/#sql-powered-data-processing)-powered bioinformatic data querying or manipulation\n* native parallel engine powered by Apache DataFusion and [sequila-native](https://github.com/biodatageeks/sequila-native)\n* [out-of-core/streaming](https://biodatageeks.org/polars-bio/features/#streaming) processing (for data too large to fit into a computer's main memory)  with [Apache DataFusion](https://datafusion.apache.org/) and [polars](https://pola.rs/)\n* support for *federated* and *streamed* reading data from [cloud storages](https://biodatageeks.org/polars-bio/features/#cloud-storage) (e.g. S3, GCS) with [Apache OpenDAL](https://github.com/apache/opendal) enabling processing large-scale genomics data without materializing in memory\n* zero-copy data exchange with [Apache Arrow](https://arrow.apache.org/)\n* bioinformatics file [formats](https://biodatageeks.org/polars-bio/features/#file-formats-support) with [noodles](https://github.com/zaeleus/noodles) and [exon](https://github.com/wheretrue/exon)\n* fast overlap operations with [COITrees: Cache Oblivious Interval Trees](https://github.com/dcjones/coitrees)\n* pre-built wheel packages for *Linux*, *Windows* and *MacOS* (*arm64* and *x86_64*) available on [PyPI](https://pypi.org/project/polars-bio/#files)\n\n## Single-thread performance 🏃‍\n![overlap-single.png](docs/assets/overlap-single.png)\n\n![overlap-single.png](docs/assets/nearest-single.png)\n\n![count-overlaps-single.png](docs/assets/count-overlaps-single.png)\n\n![coverage-single.png](docs/assets/coverage-single.png)\n\n## Parallel performance 🏃‍🏃‍\n![overlap-parallel.png](docs/assets/overlap-parallel.png)\n\n![overlap-parallel.png](docs/assets/nearest-parallel.png)\n\n![count-overlaps-parallel.png](docs/assets/count-overlaps-parallel.png)\n\n![coverage-parallel.png](docs/assets/coverage-parallel.png)\n\n\n## Citing\n\nIf you use **polars-bio** in your work, please cite:\n\n```bibtex\n@article {Wiewiorka2025.03.21.644629,\n\tauthor = {Wiewiorka, Marek and Khamutou, Pavel and Zbysinski, Marek and Gambin, Tomasz},\n\ttitle = {polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets},\n\telocation-id = {2025.03.21.644629},\n\tyear = {2025},\n\tdoi = {10.1101/2025.03.21.644629},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2025/03/25/2025.03.21.644629},\n\teprint = {https://www.biorxiv.org/content/early/2025/03/25/2025.03.21.644629.full.pdf},\n\tjournal = {bioRxiv}\n}\n```\n\nRead the [documentation](https://biodatageeks.github.io/polars-bio/)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiodatageeks%2Fpolars-bio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiodatageeks%2Fpolars-bio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiodatageeks%2Fpolars-bio/lists"}