{"id":19154477,"url":"https://github.com/bcgsc/transabyss","last_synced_at":"2025-05-07T06:40:28.962Z","repository":{"id":18435853,"uuid":"21623148","full_name":"bcgsc/transabyss","owner":"bcgsc","description":"de novo assembly of RNA-seq data using ABySS","archived":false,"fork":false,"pushed_at":"2023-07-21T02:39:34.000Z","size":741,"stargazers_count":34,"open_issues_count":4,"forks_count":14,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-04-19T19:34:38.894Z","etag":null,"topics":["bioinformatics","rna-seq","transcriptome","transcriptome-assembly"],"latest_commit_sha":null,"homepage":"","language":"Python","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/bcgsc.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}},"created_at":"2014-07-08T17:42:46.000Z","updated_at":"2024-09-21T12:28:36.000Z","dependencies_parsed_at":"2023-10-20T18:19:26.825Z","dependency_job_id":null,"html_url":"https://github.com/bcgsc/transabyss","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2Ftransabyss","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2Ftransabyss/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2Ftransabyss/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2Ftransabyss/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bcgsc","download_url":"https://codeload.github.com/bcgsc/transabyss/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252830201,"owners_count":21810765,"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":["bioinformatics","rna-seq","transcriptome","transcriptome-assembly"],"created_at":"2024-11-09T08:27:00.684Z","updated_at":"2025-05-07T06:40:28.921Z","avatar_url":"https://github.com/bcgsc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Release](https://img.shields.io/github/release/bcgsc/transabyss.svg)](https://github.com/bcgsc/transabyss/releases)\n[![Downloads](https://img.shields.io/github/downloads/bcgsc/transabyss/total?logo=github)](https://github.com/bcgsc/transabyss/releases/download/2.0.1/transabyss-2.0.1.zip)\n[![Conda](https://img.shields.io/conda/dn/bioconda/transabyss?label=Conda)](https://anaconda.org/bioconda/transabyss)\n[![Issues](https://img.shields.io/github/issues/bcgsc/transabyss.svg)](https://github.com/bcgsc/transabyss/issues)\n\n# Trans-ABySS\n## *De novo* assembly of RNAseq data using ABySS\n\n[Ka Ming Nip](mailto:kmnip@bcgsc.ca) and [Readman Chiu](mailto:rchiu@bcgsc.ca)\n\nCopyright 2018 Canada's Michael Smith Genome Sciences Centre, BC Cancer\n\nPlease use our [Google Group](mailto:trans-abyss@googlegroups.com) for [discussions and\nsupport](https://groups.google.com/d/forum/trans-abyss).\n  \nYou may also create [issues](https://github.com/bcgsc/transabyss/issues) on our GitHub repository.\n\nIf you use Trans-ABySS, please cite:\n\n[Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)](http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1517.html)\n\n--------------------------------------------------------------------------------\n\nProgram requirements for `transabyss` and `transabyss-merge`:\n  * [ABySS 2.0.x](https://github.com/bcgsc/abyss/releases)\n  * [Python 2.7.x](https://www.python.org/download/releases/2.7.14/) or [Python 3.6.x](https://www.python.org/download/releases/3.6.4/)\n  * [python-igraph 0.7.x](http://igraph.org/python/#downloads)\n  * [BLAT](http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat)\n\nRequired Python packages (ie. python-igraph) can be installed\neasily with `pip`, ie.\n\n```\npip install igraph\n```\n\nOther required softwares must be accessible from your `PATH` environment variable.\n\nTo test `transabyss` on our sample dataset:\n\n```\nbash sample_dataset/assemble.sh\n```  \n  \nPlease check out our [short tutorial](TUTORIAL.md) for more information on the usage of each application.\n\n\n--------------------------------------------------------------------------------\nEOF\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Ftransabyss","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbcgsc%2Ftransabyss","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Ftransabyss/lists"}