{"id":13606297,"url":"https://github.com/biowasm/biowasm","last_synced_at":"2025-04-12T08:30:52.670Z","repository":{"id":37209706,"uuid":"206987038","full_name":"biowasm/biowasm","owner":"biowasm","description":"WebAssembly modules for genomics","archived":false,"fork":false,"pushed_at":"2024-11-01T17:51:20.000Z","size":5317,"stargazers_count":217,"open_issues_count":5,"forks_count":23,"subscribers_count":10,"default_branch":"main","last_synced_at":"2024-11-01T18:30:34.577Z","etag":null,"topics":["awk","bedtools","bioinformatics","bowtie2","genomics","grep","javascript","jq","minimap2","samtools","sed","seqtk","webassembly"],"latest_commit_sha":null,"homepage":"https://biowasm.com","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biowasm.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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}},"created_at":"2019-09-07T15:24:26.000Z","updated_at":"2024-10-22T23:13:11.000Z","dependencies_parsed_at":"2023-02-18T18:46:19.489Z","dependency_job_id":"8fb63ab0-8e8e-4395-b2ce-c4473e558b8b","html_url":"https://github.com/biowasm/biowasm","commit_stats":{"total_commits":1010,"total_committers":9,"mean_commits":"112.22222222222223","dds":0.09108910891089106,"last_synced_commit":"31c95aa82c861560edad335251e3234ebb0e60a8"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biowasm%2Fbiowasm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biowasm%2Fbiowasm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biowasm%2Fbiowasm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biowasm%2Fbiowasm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biowasm","download_url":"https://codeload.github.com/biowasm/biowasm/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248539781,"owners_count":21121231,"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","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":["awk","bedtools","bioinformatics","bowtie2","genomics","grep","javascript","jq","minimap2","samtools","sed","seqtk","webassembly"],"created_at":"2024-08-01T19:01:07.902Z","updated_at":"2025-04-12T08:30:47.660Z","avatar_url":"https://github.com/biowasm.png","language":"HTML","readme":"![biowasm logo](https://avatars.githubusercontent.com/u/62475458?s=200\u0026v=4)\n\n# biowasm\n\n![Tests](https://github.com/biowasm/biowasm/workflows/Tests/badge.svg)\n![Deploy](https://github.com/biowasm/biowasm/workflows/Deploy%20biowasm%20v3/badge.svg)\n\nA repository of genomics tools, compiled from C/C++ to WebAssembly so they can run in a web browser.\n\n## Getting started\n\n* [Documentation](https://biowasm.com/documentation)\n* [List of supported packages](https://biowasm.com/cdn)\n\n## Who uses biowasm?    \n\n| Tool | Why biowasm? |\n|-|-|\n| [sandbox.bio](https://sandbox.bio) | Runs command-line tools in the browser to power interactive tutorials |\n| [42basepairs](https://42basepairs.com) | Runs `samtools`, `bedtools`, `bcftools` and other tools to preview genomic files |\n| [CZ ID](https://czid.org/) ([repo](https://github.com/chanzuckerberg/czid-web)) | Runs `htsfile` and `seqtk` to identify data issues before file upload |\n| [Nanopore](https://bonito.epi2me.io) | Runs `samtools` to generate `.bam` files after basecalling in the browser |\n| [ViralWasm](https://niema-lab.github.io/ViralWasm/) ([repo](https://github.com/Niema-Lab/ViralWasm)) | Runs `minimap2` and `ViralConsensus` for viral molecular epidemiology analysis |\n| [Datagrok](https://datagrok.ai) ([repo](https://github.com/datagrok-ai/public)) | Runs `kalign` in the browser for multiple-sequence alignment analysis |\n| [bedqc](https://quinlan-lab.github.io/bedqc) ([repo](https://github.com/quinlan-lab/bedqc)) | Runs `bedtools` in the browser to validate BED files |\n| [Ribbon](https://genomeribbon.com) ([repo](https://github.com/MariaNattestad/Ribbon)) | Runs `samtools` in the browser to parse, estimate coverage and subsample BAM files |\n| [fastq.bio](https://www.fastq.bio) ([repo](https://github.com/robertaboukhalil/fastq.bio)) | Runs `fastp` in the browser to evaluate sequencing data quality |\n\n## How it works\n\n| Tool | Description | Link |\n|-|-|-|\n| biowasm | Recipes for compiling C/C++ genomics tools to WebAssembly | This repo |\n| biowasm CDN | Free server hosting pre-compiled tools for use in your apps | [biowasm.com/cdn](https://biowasm.com/cdn) |\n| Aioli | Tool for running these modules in a browser, inside WebWorkers | [biowasm/aioli](https://github.com/biowasm/aioli) |\n\n\n## Logo\n\n* Logo by [tinygraphs](https://www.tinygraphs.com/#?name=biowasm\u0026shape=labs%2Fisogrids%2Fhexa\u0026theme=seascape\u0026numcolors=4#tryitout)\n\n## Contributing\n\nSee [CONTRIBUTING.md](https://github.com/biowasm/biowasm/blob/main/CONTRIBUTING.md).\n","funding_links":[],"categories":["HTML","Genomics Software"],"sub_categories":["Articles and References"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiowasm%2Fbiowasm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiowasm%2Fbiowasm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiowasm%2Fbiowasm/lists"}