{"id":20153573,"url":"https://github.com/seqan/stellar3","last_synced_at":"2026-02-03T21:04:33.339Z","repository":{"id":133217371,"uuid":"599103200","full_name":"seqan/stellar3","owner":"seqan","description":"the SwifT Exact LocaL AligneR","archived":false,"fork":false,"pushed_at":"2024-12-12T15:24:26.000Z","size":154304,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-07-13T05:40:36.548Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/seqan.png","metadata":{"files":{"readme":"README.md","changelog":null,"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}},"created_at":"2023-02-08T13:12:08.000Z","updated_at":"2024-12-12T14:59:47.000Z","dependencies_parsed_at":"2024-01-04T11:32:28.505Z","dependency_job_id":"6f4fb3ae-18c1-4f14-aeb6-dbb92731b856","html_url":"https://github.com/seqan/stellar3","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/seqan/stellar3","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fstellar3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fstellar3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fstellar3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fstellar3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/stellar3/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fstellar3/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29057119,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T20:13:53.544Z","status":"ssl_error","status_checked_at":"2026-02-03T20:13:40.507Z","response_time":96,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2024-11-13T23:19:46.560Z","updated_at":"2026-02-03T21:04:33.312Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# STELLAR3 - the SwifT Exact LocaL AligneR\nThis is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but uses the [sharg parser](https://docs.seqan.de/seqan3/3-master-user/tutorial_argument_parser.html) and can be used to narrow the search to only a segment of the reference database.\n\n## Building Stellar3:\n1. clone this repository: `git clone --recurse-submodules https://github.com/seqan/stellar3`\n2. create a build directory and visit it: `mkdir stellar3/build \u0026\u0026 cd $_`\n3. run cmake: `cmake ..`\n4. build the application: `make`\n5. show the help page: `./bin/stellar --help`\n\n## Running Stellar3:\nThe `example` folder contains example data for a test run. Stellar3 can be used to produce soft-clipped read alignments or to find all local alignments between two genomes.\n\nSearching the reference sequences for local alignments with a minimum length of 50 and a maximum error rate of 0.02:\n`./bin/stellar -e 0.02 -l 50 -o mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`\n\nSearching only a segment of the reference for local alignments:\n`./bin/stellar --sequenceOfInterest 0 --segmentBegin 5000 --segmentEnd 7500 -e 0.02 -l 50 -o segment.mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`\n\nFinding all local alignments between two related genomes:\n`./bin/stellar -e 0.1 -l 50 -o alignments.gff ../example/NC_001474.fasta ../example/NC_001477.fasta`\n\nSee the original [documentation](https://github.com/seqan/seqan/tree/main/apps/stellar) for details on the Stellar output formats.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fstellar3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fstellar3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fstellar3/lists"}