{"id":18666765,"url":"https://github.com/bionode/bionode-bwa","last_synced_at":"2025-04-11T23:33:11.470Z","repository":{"id":17179466,"uuid":"19946825","full_name":"bionode/bionode-bwa","owner":"bionode","description":"A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).","archived":false,"fork":false,"pushed_at":"2017-06-01T22:53:08.000Z","size":352,"stargazers_count":7,"open_issues_count":1,"forks_count":3,"subscribers_count":24,"default_branch":"master","last_synced_at":"2025-03-25T19:53:19.215Z","etag":null,"topics":["bioinformatics","bionode","nodejs","tool","wrapper"],"latest_commit_sha":null,"homepage":"bionode.io","language":"JavaScript","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/bionode.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-05-19T15:19:41.000Z","updated_at":"2020-03-13T13:56:54.000Z","dependencies_parsed_at":"2022-09-11T02:23:00.616Z","dependency_job_id":null,"html_url":"https://github.com/bionode/bionode-bwa","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionode%2Fbionode-bwa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionode%2Fbionode-bwa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionode%2Fbionode-bwa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionode%2Fbionode-bwa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bionode","download_url":"https://codeload.github.com/bionode/bionode-bwa/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248262400,"owners_count":21074300,"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":["bioinformatics","bionode","nodejs","tool","wrapper"],"created_at":"2024-11-07T08:33:59.637Z","updated_at":"2025-04-11T23:33:06.456Z","avatar_url":"https://github.com/bionode.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003ca href=\"http://bionode.io\"\u003e\n    \u003cimg height=\"200\" width=\"200\" title=\"bionode\" alt=\"bionode logo\" src=\"https://rawgithub.com/bionode/bionode/master/docs/bionode-logo.min.svg\"/\u003e\n  \u003c/a\u003e\n  \u003cbr/\u003e\n  \u003ca href=\"http://bionode.io/\"\u003ebionode.io\u003c/a\u003e\n\u003c/p\u003e\n\n\n# bionode-bwa\n\n\u003e A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).\n\n[![npm](https://img.shields.io/npm/v/bionode-bwa.svg?style=flat-square)](http://npmjs.org/package/bionode-bwa)[![Build Status][travis-image]][travis-url]\n[![Travis](https://img.shields.io/travis/bionode/bionode-bwa.svg?style=flat-square)](https://travis-ci.org/bionode/bionode-bwa)\n[![Coveralls](https://img.shields.io/coveralls/bionode/bionode-bwa.svg?style=flat-square)](http://coveralls.io/r/bionode/bionode-bwa)\n[![Dependencies](http://img.shields.io/david/bionode/bionode-bwa.svg?style=flat-square)](http://david-dm.org/bionode/bionode-bwa)\n[![npm](https://img.shields.io/npm/dt/bionode-bwa.svg?style=flat-square)](https://www.npmjs.com/package/bionode-bwa)\n[![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg?style=flat-square)](https://gitter.im/bionode/bionode-bwa)\n\n\n## Install\n\nYou need to install the latest Node.JS first, please check [nodejs.org](http://nodejs.org) or do the following:\n\n```bash\n# Ubuntu\nsudo apt-get install npm\n# Mac\nbrew install node\n# Both\nnpm install -g n\nn stable\n```\n\nTo use `bionode-bwa` as a command line tool, you can install it globally with `-g`.\n\n```bash\nnpm install bionode-bwa -g\n```\n\nOr, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the `node_modules` directory by doing the same command **without** `-g`.\n\n```bash\nnpm i bionode-bwa # 'i' can be used as shorcut to 'install'\n```\n\n\n## Usage\n\nIf you're using bionode-bwa with Node.js, you can require the module:\n\n```js\nvar bwa = require('bionode-bwa')\n// aligment path is optional, reads name used instead with sam suffix\nbwa('reference.fasta.gz', 'reads.fastq.gz', 'alignment.sam')\n.on('data', console.log)\n```\n\n```js\nvar options = {\n  operation: 'mem',\n  params: '-t 4'\n}\nvar stream = bwa(options) // Use BWA mem algorithm with 4 threads\nvar obj = {\n  reference: 'reference.fasta.gz',\n  reads: ['reads.fastq.gz']\n}\nstream.write(obj)\n```\n\nPlease read the [documentation](http://rawgit.com/bionode/bionode-bwa/master/docs/bionode-bwa.html) for the methods exposed by bionode-bwa.  \nCheck [BWA's documentation](http://bio-bwa.sourceforge.net/bwa.shtml) for the arguments that can be passed.\n\n\n### Command line examples\n\n```sh\n$ bionode-bwa reference.fasta.gz reads.fastq.gz --alignment out.sam\n$ echo '{\"reference\": \"ref.fasta.gz\", \"reads\": \"[p1.fq, p2.fq]\"}' | bionode-bwa  -\n```\n\n\n## Contributing\n\nWe welcome all kinds of contributions at all levels of experience, please read the [CONTRIBUTING.md](CONTRIBUTING.md) to get started!\n\n\n## Communication channels\n\nDon't be shy! Come talk to us :smiley:\n\n* **Email** [mail@bionode.io](mailto:mail@bionode.io)\n* **Chat room** [http://gitter.im/bionode/bionode](http://gitter.im/bionode/bionode)\n* **IRC** #bionode on Freenode\n* **Twitter** [@bionode](http://twitter.com/@bionode)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionode%2Fbionode-bwa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionode%2Fbionode-bwa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionode%2Fbionode-bwa/lists"}