{"id":38674013,"url":"https://github.com/wglab/seqmule","last_synced_at":"2026-01-17T10:00:20.727Z","repository":{"id":17519766,"uuid":"20307753","full_name":"WGLab/SeqMule","owner":"WGLab","description":"Automated human exome/genome variants detection from FASTQ files","archived":false,"fork":false,"pushed_at":"2021-09-27T12:39:36.000Z","size":26124,"stargazers_count":23,"open_issues_count":48,"forks_count":23,"subscribers_count":13,"default_branch":"master","last_synced_at":"2026-01-14T01:53:44.253Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://seqmule.usc.edu","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/WGLab.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}},"created_at":"2014-05-29T20:39:30.000Z","updated_at":"2025-09-16T19:16:04.000Z","dependencies_parsed_at":"2022-09-05T15:41:29.097Z","dependency_job_id":null,"html_url":"https://github.com/WGLab/SeqMule","commit_stats":null,"previous_names":["wanggenomicslab/seqmule"],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/WGLab/SeqMule","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FSeqMule","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FSeqMule/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FSeqMule/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FSeqMule/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/WGLab","download_url":"https://codeload.github.com/WGLab/SeqMule/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WGLab%2FSeqMule/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":"2026-01-17T10:00:18.814Z","updated_at":"2026-01-17T10:00:20.593Z","avatar_url":"https://github.com/WGLab.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"![SeqMule](img/seqmule.png)\n# SeqMule: Automated human exome/genome variants detection\n\nSeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.\n\n## Features\n\n* Mendelian disease and cancer genome analysis\n  \n   Suitable for both Mendelian disease study and tumor-normal paired somatic mutation analysis\n\n* Multiple aligners\n\n   BWA-MEM, BWA-BACKTRACK, Bowtie, Bowtie2, SOAP2, SNAP\n\n* Multiple variant callers\n\n   GATK, SAMtools, VarScan, SOAPsnp, Freebayes are available.\n\n   As stated on 1000 Genomes Project website, genotypes obtained through a consensus procedure are estimated to have 30% fewer errors than those generated by any single caller. \n\n   As we have demonstrated in a previous study (O'Rawe et al. *Genome Med* 2013, **5**:28), consensus calls from multiple calling algorithms may increase calling accuracy and reduce Mendelian error rates.\n\n* Easy downloading and installation.\n\n   Most jobs can be done with one-line command.\n\n* Fast and easy customization\n\n   Just use predefined `advanced_config` or change it yourself!\n\n* Sun Grid Engine (SGE) integration\n\n   SeqMule is scalable and can utilize cluster computation resources managed by SGE.\n\n\n## Synopsis\n\n* **seqmule download**: download databases/BEDs that are required by sequence alignment or variant calling software tools\n\n* **seqmule pipeline**: perform the automated pipeline for detection of variants from whole-exome/genome data\n\n* **seqmule stats**: perform statistical analysis of variants data, such as drawing Venn diagram to examine overlap between VCF files, generating union/consensus ca\nlls, generating coverage/alignment statistics in specific genomic regions, calculating Mendelian error rates\n\n* **seqmule run**: continue run from last executed step after interruption or run from a specific step\n\n* **seqmule update**: perform automated update of the SeqMule software tools\n**See `doc/User Manual/Manuals` for details**\n\n\n## Docker image\nhttps://hub.docker.com/repository/docker/genomicslab/seqmule\n\n## Revision History\n\nFor release history, please visit [here](https://github.com/WGLab/SeqMule/releases). For details, please go [here](https://github.com/WangGenomicsLab/SeqMule/commits/master).\n\n## Contact\n\nFor questions/bugs/issues, please post on [GitHub](https://github.com/WGLab/SeqMule/issues). In general, please do NOT send questions to our email. Your question may be very likely to help other users.\n\nPlease join [SeqMule-dev](https://groups.google.com/forum/#!forum/seqmule-dev) for updates.\n\n## Citation\n\nGuo Y, Ding X, Shen Y, Lyon GJ, Wang K. [SeqMule: automated human exome/genome variants detection](http://www.nature.com/articles/srep14283). Scientific Reports, doi: 10.1038/srep14283, 2015\n\n## More information\n\n* [SeqMule Homepage](http://seqmule.openbioinformatics.org)\n\n* [Wang Genomics Lab Homepage](http://wglab.org)\n\n\n\nCopyright 2014-2021 [USC Wang Lab](http://wglab.org)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwglab%2Fseqmule","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwglab%2Fseqmule","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwglab%2Fseqmule/lists"}