{"id":38676427,"url":"https://github.com/wglab/infuse","last_synced_at":"2026-01-17T10:01:10.061Z","repository":{"id":276198344,"uuid":"823313723","full_name":"WGLab/InFuse","owner":"WGLab","description":"Software for detecting gene fusions and exon-skippings from long read sequencing","archived":false,"fork":false,"pushed_at":"2025-03-11T21:34:37.000Z","size":45,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-03-11T22:25:23.810Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/WGLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2024-07-02T19:50:40.000Z","updated_at":"2025-03-11T21:34:40.000Z","dependencies_parsed_at":"2025-02-06T21:19:53.849Z","dependency_job_id":"7ae5e3ed-605f-4812-8ce2-45f4cbed0d73","html_url":"https://github.com/WGLab/InFuse","commit_stats":null,"previous_names":["wglab/infuse"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/WGLab/InFuse","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FInFuse","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FInFuse/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FInFuse/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FInFuse/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/WGLab","download_url":"https://codeload.github.com/WGLab/InFuse/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FInFuse/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28505570,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T06:57:29.758Z","status":"ssl_error","status_checked_at":"2026-01-17T06:56:03.931Z","response_time":85,"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":"2026-01-17T10:00:53.956Z","updated_at":"2026-01-17T10:01:09.991Z","avatar_url":"https://github.com/WGLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# InFuse\nInFuse: gene fusion and exon-skipping detection from long read sequencing (under construction)\n![overview](https://github.com/user-attachments/assets/25b97717-ad02-4125-896e-203dd038a7cc)\n\n## Installation\n```\ngit clone https://github.com/WGLab/InFuse.git\npip install numpy pandas numba sklearn pysam ncls numpy_indexed parasail\npython InFuse/InFuse.py --help\n```\n## Usage\n\nFor gene fusion detection, please run the following command:\n\n`python PATH_TO_INFUSE_REPO/InFuse.py --bam BAM_FILE --output OUTPUT_FOLDER --prefix PREFIX --gff GFF_ANNOTATION_FILE --transcripts TRANSCRIPT_FASTA_FILE --threads NUM_THREADS --min_support MIN_READS --distance_threshold DISTANCE_THRESHOLD --gf_only`\n\nwhere BAM_FILE is an aligned BAM file, GFF_ANNOTATION_FILE is genome annotation GFF3 file, TRANSCRIPT_FASTA_FILE is a FASTA file containing spliced transcript sequences from the GFF3 file, NUM_THREADS is the number of threads to use for multiprocessing speedup, MIN_READS specifies the minimum read support needed for reporting a gene fusion, and DISTANCE_THRESHOLD specifies the distance in bp for merging gene fusion breakpoints.\n\nThe output folder will contain a tab seperated file `PREFIX.final_gf_double_bp` containing all gene fusions, as well as a python pickle file `PREFIX.final_gf_double_bp.pickle` containing detailed read-level information for all  gene fusions.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwglab%2Finfuse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwglab%2Finfuse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwglab%2Finfuse/lists"}