{"id":17844814,"url":"https://github.com/dombennett/project-cluster","last_synced_at":"2025-07-04T23:03:53.897Z","repository":{"id":68567007,"uuid":"123279860","full_name":"DomBennett/Project-cluster","owner":"DomBennett","description":":hibiscus: Short pipeline for counting number of clusters across .sam files","archived":false,"fork":false,"pushed_at":"2018-05-07T12:38:31.000Z","size":20,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-08T06:12:58.622Z","etag":null,"topics":["cdhit","clustering","pipeline","polyploid"],"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/DomBennett.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":"2018-02-28T12:08:37.000Z","updated_at":"2018-05-07T12:38:33.000Z","dependencies_parsed_at":null,"dependency_job_id":"74b47e19-7f5b-4feb-9df1-a26296cbbdd5","html_url":"https://github.com/DomBennett/Project-cluster","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-cluster","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-cluster/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-cluster/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-cluster/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/Project-cluster/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246837685,"owners_count":20841903,"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":["cdhit","clustering","pipeline","polyploid"],"created_at":"2024-10-27T21:33:07.503Z","updated_at":"2025-04-02T15:12:34.569Z","avatar_url":"https://github.com/DomBennett.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Project-cluster\n\nIdentify and count clusters across a series of .sam files.\n\n## Usage\n\n`python run.py --help`\n\n## Install\n\n`git clone https://github.com/DomBennett/Project-cluster.git`\n\nOr download the zipped folder:\n\n`wget https://github.com/DomBennett/Project-cluster/archive/master.zip`\n\n## Requirements\n\n* One .sam file stored per folder\n* cdhit\n* Python (v2 or v3)\n\n## Steps\n\n* Convert .sam to .fasta by extracting the orthologous sequence identified within\nthe .sam file.\n* Run cdhit\n* Count clusters with greater than `min_nsqs`\n* Report number of clusters per .sam in a .csv\n\n## Authors\n\nD.J. Bennett \u0026 J.S. Eriksson\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-cluster","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fproject-cluster","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-cluster/lists"}