{"id":25501955,"url":"https://github.com/opengene/pecheck","last_synced_at":"2025-06-30T05:05:54.006Z","repository":{"id":90140196,"uuid":"142528663","full_name":"OpenGene/pecheck","owner":"OpenGene","description":"check paired-end FASTQ data integrity","archived":false,"fork":false,"pushed_at":"2018-08-01T02:18:58.000Z","size":85,"stargazers_count":6,"open_issues_count":1,"forks_count":3,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-10T09:54:06.304Z","etag":null,"topics":["bioinformatics","check","consistence","fastq","identical","illumina","integrity","paired-end","pe"],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenGene.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-07-27T04:44:00.000Z","updated_at":"2022-05-04T08:35:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"3353ce57-f834-4e00-b47d-1665b5c3918d","html_url":"https://github.com/OpenGene/pecheck","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/OpenGene/pecheck","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fpecheck","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fpecheck/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fpecheck/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fpecheck/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenGene","download_url":"https://codeload.github.com/OpenGene/pecheck/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fpecheck/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262714505,"owners_count":23352465,"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","check","consistence","fastq","identical","illumina","integrity","paired-end","pe"],"created_at":"2025-02-19T04:59:46.856Z","updated_at":"2025-06-30T05:05:53.979Z","avatar_url":"https://github.com/OpenGene.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pecheck\nA tool to check paired-end FASTQ data integrity\n\n# usage\nJust specify the read1 file by `-i` and the read2 file by `-I`. The input file can be gzipped (i.e. R1.fq.gz).\n```\npecheck -i R1.fq -I R2.fq\n```\nA JSON report will be then generated. If the check is passed, the JSON result will be like:\n```json\n{\n\t\"result\":\"passed\",\n\t\"message\":\"\",\n\t\"read1_num\":1000,\n\t\"read2_num\":1000,\n\t\"read1_bases\":108040,\n\t\"read2_bases\":109141\n}\n```\nAnd if it's failed, the JSON result will be like:\n```json\n{\n\t\"result\":\"failed\",\n\t\"message\":\"Numbers of read1 and read2 are different\",\n\t\"read1_num\":999,\n\t\"read2_num\":1000,\n\t\"read1_bases\":107923,\n\t\"read2_bases\":109141\n}\n```\nThe file name of the JSON report is `pecheck.json` by default, and it can be specified by `-j`. The JSON result is also printed on the terminal (STDOUT).\n\n# get pecheck\n## download binary \nThis binary is only for Linux systems: http://opengene.org/pecheck/pecheck\n```shell\n# this binary was compiled on CentOS, and tested on CentOS/Ubuntu\nwget http://opengene.org/pecheck/pecheck\nchmod a+x ./pecheck\n```\n## or compile from source\n```shell\n# get source (you can also use browser to download from master or releases)\ngit clone https://github.com/OpenGene/pecheck.git\n\n# build\ncd pecheck\nmake\n\n# Install\nsudo make install\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengene%2Fpecheck","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopengene%2Fpecheck","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengene%2Fpecheck/lists"}