{"id":43927053,"url":"https://github.com/algbio/founderblockgraphs","last_synced_at":"2026-02-06T23:09:05.846Z","repository":{"id":76973100,"uuid":"262261342","full_name":"algbio/founderblockgraphs","owner":"algbio","description":"Constructs segment repeat-free founder block graphs from multiple sequence alignments","archived":false,"fork":false,"pushed_at":"2025-07-16T09:47:06.000Z","size":233,"stargazers_count":3,"open_issues_count":1,"forks_count":1,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-07-17T13:27:11.032Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/algbio.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":"2020-05-08T07:53:52.000Z","updated_at":"2025-03-22T12:26:31.000Z","dependencies_parsed_at":"2025-03-19T00:22:50.953Z","dependency_job_id":null,"html_url":"https://github.com/algbio/founderblockgraphs","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/algbio/founderblockgraphs","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/algbio%2Ffounderblockgraphs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/algbio%2Ffounderblockgraphs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/algbio%2Ffounderblockgraphs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/algbio%2Ffounderblockgraphs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/algbio","download_url":"https://codeload.github.com/algbio/founderblockgraphs/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/algbio%2Ffounderblockgraphs/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29179641,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T22:12:24.066Z","status":"ssl_error","status_checked_at":"2026-02-06T22:12:09.859Z","response_time":59,"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":"2026-02-06T23:09:05.766Z","updated_at":"2026-02-06T23:09:05.833Z","avatar_url":"https://github.com/algbio.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# founderblockgraphs\nConstructs repeat-free/semi-repeat-free non-elastic/elastic founder graphs from multiple sequence alignments.\n\n# getting started\nClone this repository with dependencies:\n```\n$ git clone --recurse-submodules https://github.com/algbio/founderblockgraphs.git\n$ cd founderblockgraphs\n```\n\nBuild sdsl-lite-v3:\n```\n$ cd sdsl-lite-v3\n$ ./install.sh .\n$ cd ..\n```\n\nBuild this project (`founderblockgraph`, `locate_multiple`, `locate_patterns`):\n```\n$ make\n```\n\n# usage\n```\nUsage: founderblockgraph --input=MSA.fasta --output={MSA.index|efg.xgfa} [--gfa]\n[--elastic] [--gap-limit=GAPLIMIT] [--threads=THREADNUM]\n[--graphviz-output=efg.dot] [--output-paths] [--ignore-chars=\"ALPHABET\"]\nConstructs a semi-repeat-free (Elastic) Founder Graph\n\nInput is MSA given in fasta format. In standard mode (without --elastic), rows\nwith runs of gaps ‘-’ or N’s ≥ GAPLIMIT will be filtered out.\n\n  -h, --help                    Print help and exit\n      --full-help               Print help, including hidden options, and exit\n  -V, --version                 Print version and exit\n      --input=filename          MSA input path\n      --output=filename         Index/EFG output path\n      --gap-limit=GAPLIMIT      Gap limit (suppressed by --elastic)\n                                  (default=`1')\n      --graphviz-output=filename\n                                Graphviz output path\n      --memory-chart-output=filename\n                                Memory chart output path\n  -e, --elastic                 Min-max-length semi-repeat-free segmentation\n                                  (default=off)\n      --gfa                     Saves output in xGFA format  (default=off)\n  -p, --output-paths            Print the original sequences as paths of the\n                                  xGFA graph (requires --gfa)  (default=off)\n      --ignore-chars=STRING     Ignore these characters for the indexability\n                                  property/pattern matching\n  -t, --threads=THREADNUM       Max # threads  (default=`-1')\n```\n\n# todo\n - document EFG tricks related to option `--ignore-chars`, to the start and end of sequences, and to initial and ending runs of gaps\n - implement validation of .gfa files\n - implement pattern matching (`locate_multiple`, `locate_patterns`) on EFGs\n - implement min max height segmentation\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falgbio%2Ffounderblockgraphs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falgbio%2Ffounderblockgraphs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falgbio%2Ffounderblockgraphs/lists"}