{"id":16636645,"url":"https://github.com/cchd0001/genomesequencesimulator","last_synced_at":"2026-04-25T01:32:16.243Z","repository":{"id":151738580,"uuid":"96704429","full_name":"cchd0001/GenomeSequenceSimulator","owner":"cchd0001","description":"A simulator to genarate WSG data from refrence","archived":false,"fork":false,"pushed_at":"2017-07-14T07:20:04.000Z","size":1023,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-27T10:32:34.746Z","etag":null,"topics":["simulator","wgs"],"latest_commit_sha":null,"homepage":"","language":"C++","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/cchd0001.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":"2017-07-09T18:50:27.000Z","updated_at":"2025-07-07T15:39:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"8ae26ebf-2f99-43b6-bb87-28f3e8404e08","html_url":"https://github.com/cchd0001/GenomeSequenceSimulator","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cchd0001/GenomeSequenceSimulator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cchd0001%2FGenomeSequenceSimulator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cchd0001%2FGenomeSequenceSimulator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cchd0001%2FGenomeSequenceSimulator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cchd0001%2FGenomeSequenceSimulator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cchd0001","download_url":"https://codeload.github.com/cchd0001/GenomeSequenceSimulator/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cchd0001%2FGenomeSequenceSimulator/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32247025,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-24T13:21:15.438Z","status":"ssl_error","status_checked_at":"2026-04-24T13:21:15.005Z","response_time":64,"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":["simulator","wgs"],"created_at":"2024-10-12T06:22:20.752Z","updated_at":"2026-04-25T01:32:16.226Z","avatar_url":"https://github.com/cchd0001.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GenomeSequenceSimulator\n\nGSS is a small tool for simulating sequence reads from a reference genome.\nA\n\n## INSTALL\n\nSimple build by cmake .\n\nHere is a build example.\nEnter ```src``` directory:\n```\n    mkdir build\n    cd build\n    cmake ..\n    make\n```\n\nBinary execute file in ```bin/Bin/GSS```\n\n## EXAMPLE\n\nAfter build success ,enter ```example``` directory and run ```example.sh``` script.\n\n## QUICK START\n\nRun GSS with ```config.json``` file . All infomations are within config.json. \n\nHere is the ```config.json``` from example\n```\n{                                       #Top level is a object !\n    \"filePath\": \"./sequence.fasta\",     #Basic genome file. \n    \"fileType\": \"fasta\",                #Genome file type.Only support fasta now.\n    \"variable\":0.0001,                   \n    \"InDel\":0.015,   \n    \"InDel_Extern\":0.3,\n    \"error\":0.0001,\n    \"output\": [                         #Array of all simulator infos.\n        {\n            \"file_name\":\"f0\",           #Output name prefix.\n            \"file_type\":\"fastq\",        #Output file type,support fasta and fastq\n            \"read_type\": \"single\",      #\n            \"read_len\": 100,            #\n            \"insert_len\": 100,          #\n            \"depth\":80                  #The expect depth of Nucleotide.\n        },\n        {\n            \"file_name\":\"f1\",\n            \"file_type\":\"fastq\",\n            \"read_type\": \"pair-end\",\n            \"read_len\": 100,\n            \"depth\":100,\n            \"insert_len\": 250\n        }\n    ]\n}\n```\n## OUTPUT \n\nHere is the top 10 lines of each file that generated by above ```config.json```\n\n```\n==\u003e f0.fastq \u003c==\n@NC_007205.1_503982_504082_0:0:0_0/2\nCTGGAACGGAGTATTCGTTTTAAAAGAGGGTGTATAAGTTTTAAAAAAAAATATTTAAGAACTATAAATATTTAACAAAAAAAATAAAGAAATATAAAAA\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_430241_430341_0:0:0_1/2\nTTTTATCAATTTTTTTTATTTAAATAGAATCAACCAAGTTCATACCCTCGCACCGAGAGGAATTTAGTTAAATTTATAAAATTTCTAGTTTAATTTCCAA\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_1139113_1139213_0:0:0_2/1\nATACATAATAAGCACTATCTCTAAAGGATTTTTTTATTTGTTTTTTAGCATTATAAATTTCAATAAATGCATTTCTCATACTATCTTCTAGACCTGAAAA\n\n==\u003e f1_0.fastq \u003c==\n@NC_007205.1_1137336_1137436_0:0:0_0/1\nCTTACACAATTATTTTGGTAGGCAATTTTACCTCTAGCAATCATTAATTGAGAATCTCTTGTGATTGGATAATGATTATCAGAATAAGAAATGCTACTTA\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_706428_706528_0:0:0_1/2\nAAAATTCAGAGGAACTCCGTAACTTTTACCTAACACTGATTTAAGTTAAAATAATCAATGAAGTAAAAAAAGTTTGTAACCTATTAGTTGTTGGGTTGTT\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_555447_555547_0:0:0_2/2\nTTTATGCCTACCTACGGTGGAGTAGGATGATGTATAAAGAATTCTTTTAAATAAATATTTCAACCTTTCAAATTATGTTTAATATTTTATAGGAGACTGA\n\n==\u003e f1_1.fastq \u003c==\n@NC_007205.1_1138736_1138836_0:0:0_0/2\nATTCATCTCGGATATATGGTTTGAGATTAGATAGAAAATAATCAAAATAATTTCAATGGAAACTATTTCCCCATTACTACTTACGTTGTAATCGATTACC\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_705028_705128_0:0:0_1/1\nTATGGCAAAATATTTGAATTCATATATAAAATTGACAAGATTAGTTTAAAAAAAAAGAAATCTATCGATTTTAAAATTATTAATGAAGCTCTTGAGGAAT\n+\niiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii\n@NC_007205.1_554047_554147_0:0:0_2/1\nTTTGATAGATTTTTAAGTTTTAAAAAATCTTTAGACCTAATTTCAAAAACTGGAATATTTATTTTTGATAATTCTGAAGGATATAATGAACCAAGAGATA\n\n```\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcchd0001%2Fgenomesequencesimulator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcchd0001%2Fgenomesequencesimulator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcchd0001%2Fgenomesequencesimulator/lists"}