{"id":28974988,"url":"https://github.com/seqan/dream-stellar","last_synced_at":"2025-10-05T04:42:58.630Z","repository":{"id":40504292,"uuid":"384363964","full_name":"seqan/dream-stellar","owner":"seqan","description":"Fast and exact local alignments","archived":false,"fork":false,"pushed_at":"2025-06-19T08:17:54.000Z","size":5082,"stargazers_count":1,"open_issues_count":11,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-06-19T09:29:34.889Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/seqan.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.md","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":"2021-07-09T07:55:13.000Z","updated_at":"2025-06-19T08:53:51.000Z","dependencies_parsed_at":"2023-09-23T14:40:54.492Z","dependency_job_id":"686ed552-ed17-46bd-bbda-fd3e44e30842","html_url":"https://github.com/seqan/dream-stellar","commit_stats":null,"previous_names":["eaasna/dream-stellar","eaasna/valik","seqan/dream-stellar"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/seqan/dream-stellar","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream-stellar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream-stellar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream-stellar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream-stellar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/dream-stellar/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream-stellar/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261669018,"owners_count":23192362,"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":[],"created_at":"2025-06-24T12:07:51.984Z","updated_at":"2025-10-05T04:42:58.621Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DREAM-Stellar [![install with bioconda][1]][2] [![build status][3]][4] [![codecov][5]][6]\n\u003c!--\n    Above uses reference-style links with numbers.\n    See also https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet#links.\n\n    For example, `[![build status][1]][2]` evaluates to the following:\n        `[link_text][2]`\n        `[2]` is a reference to a link, i.e. `[link_text](https://...)`\n\n        `[link_text]` = `[![build status][1]]`\n        `[1]` is once again a reference to a link - this time an image, i.e. `[![build status](https://...)]\n        `![build status]` is the text that should be displayed if the linked resource (`[1]`) is not available\n\n    `[![build status][1]][2]` hence means:\n    Show the picture linked under `[1]`. In case it cannot be displayed, show the text \"build status\" instead.\n    The picture, or alternative text, should link to `[2]`.\n--\u003e\n\n[1]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat \"Install with bioconda\"\n[2]: #install-with-bioconda-linux\n\u003c!--\n    This is the CI badge image:\n        `https://img.shields.io/github/workflow/status/` - we do not use GitHub's badges as they are not customisable.\n        `/seqan/dream-stellar/` - owner/repository\n        `CI%20on%20Linux` - name of the workflow as encoded URL (e.g., whitespace = %20)\n        `main` - branch to show\n        `?style=flat\u0026logo=github` - use a GitHub-style badge\n        `\u0026label=dream-stellar%20CI` - text on the badge\n        `\"Open GitHub actions page\"` - this text will be shown on hover\n--\u003e\n[3]: https://img.shields.io/github/actions/workflow/status/seqan/dream-stellar/ci_linux.yml?branch=main\u0026style=flat\u0026logo=github\u0026label=DREAM-Stellar%20CI \"Open GitHub actions page\"\n\u003c!--\n    This is the CI badge link:\n        `https://github.com/seqan/dream-stellar/actions` - actions page of owner/repository\n        `?query=branch%3Amain` - only show actions that ran on the mater branch\n--\u003e\n[4]: https://github.com/seqan/dream-stellar/actions?query=branch%3Amain\n\u003c!--\n    This is the Codecov badge image:\n        Codecov offers badges: https://app.codecov.io/gh/seqan/dream-stellar/settings/badge\n        While being logged in into Codecov, navigate to Settings-\u003eBadge and copy the markdown badge.\n        Copy the image part of the markdown badge here.\n    `\"Open Codecov page\"` - this text will be shown on hover\n--\u003e\n[5]: https://codecov.io/gh/seqan/dream-stellar/branch/main/graph/badge.svg \"Open Codecov page\"\n\u003c!--\n    This is the Codecov badge link:\n        Codecov offers badges: https://app.codecov.io/gh/seqan/dream-stellar/settings/badge\n        While being logged in into Codecov, navigate to Settings-\u003eBadge and copy the markdown badge.\n        Copy the URL part of the markdown badge here.\n--\u003e\n[6]: https://codecov.io/gh/seqan/dream-stellar\n\n## Getting started \nFind the set of local alignments between sets of reference and query sequences.\n\n`dream-stellar build test/data/dream/ref.fasta --pattern 50 --output index.ibf`\n\n`dream-stellar search --index index.ibf --query test/data/dream/query.fasta --error-rate 0.02 --output search.gff`\n\nFor a detailed list of options, see the help pages:\n```console\ndream-stellar --help\ndream-stellar build --help\ndream-stellar search --help\n```\n\n## Download and Installation\n\n### Install with [bioconda](http://bioconda.github.io/recipes/dream-stellar/README.html) (Linux)\n\n```bash\nconda install -c bioconda -c conda-forge dream-stellar\n```\n\n### Download and compile from source\n\u003cdetails\u003e\u003csummary\u003ePrerequisites (click to expand)\u003c/summary\u003e\n\n* CMake \u003e= 3.25\n* GCC 10, 11 or 12 (most recent minor version)\n* git\n\nRefer to the [Seqan3 Setup Tutorial](https://docs.seqan.de/seqan/3-master-user/setup.html) for more in depth information.\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eDownload current master branch (click to expand)\u003c/summary\u003e\n\n```bash\ngit clone https://github.com/seqan/dream-stellar\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\u003csummary\u003eBuilding (click to expand)\u003c/summary\u003e\n\n```bash\ncd dream-stellar\nmkdir -p build\ncd build\ncmake ..\nmake\n```\n\nThe binary can be found in `bin`.\n\nYou may want to add the executable to your PATH:\n```\nexport PATH=$(pwd)/bin:$PATH\nvalik --version\n```\n\n\u003c/details\u003e\n\n## DREAM-Stellar benchmark\nThe DREAM-Stellar [benchmark](https://github.com/eaasna/DREAM-stellar-benchmark/tree/v2.0) contains example workflows for using DREAM-Stellar for distributed local alignment.\n\n## Authorship and Copyright\nDREAM-Stellar is licensed under BSD 3, for details please see the [license](https://github.com/seqan/dream-stellar/blob/main/LICENSE.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fdream-stellar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fdream-stellar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fdream-stellar/lists"}