{
  "_id": "6ac8f765de46216d5edd941a",
  "Package": "Rfastp",
  "Type": "Package",
  "Title": "An Ultra-Fast and All-in-One Fastq Preprocessor (Quality\nControl, Adapter, low quality and polyX trimming) and UMI\nSequence Parsing).",
  "Version": "1.23.0",
  "Authors@R": "c(\nperson(\"Wei\", \"Wang\",\nemail=\"periwinkle.david@gmail.com\",\nrole=c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-3216-7118\")),\nperson(\"Ji-Dung\", \"Luo\",\nemail=\"jluo@rockefeller.edu\",\nrole=c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-0150-1440\")),\nperson(\"Thomas\", \"Carroll\",\nemail=\"tc.infomatics@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-0073-1714\")))",
  "Description": "Rfastp is an R wrapper of fastp developed in c++. fastp\nperforms quality control for fastq files. including low quality\nbases trimming, polyX trimming, adapter auto-detection and\ntrimming, paired-end reads merging, UMI sequence/id handling.\nRfastp can concatenate multiple files into one file (like shell\ncommand cat) and accept multiple files as input.",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "biocViews": "QualityControl, Sequencing, Preprocessing, Software",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:22 UTC",
  "RemoteUrl": "https://github.com/bioc/Rfastp",
  "RemoteRef": "HEAD",
  "RemoteSha": "e419718a583a352c9456d9b7918fdd3a66e639ce",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-09 14:09:25 UTC",
    "User": "root"
  },
  "Author": "Wei Wang [cre, aut] (ORCID: <https://orcid.org/0000-0002-3216-7118>),\nJi-Dung Luo [ctb] (ORCID: <https://orcid.org/0000-0003-0150-1440>),\nThomas Carroll [aut] (ORCID: <https://orcid.org/0000-0002-0073-1714>)",
  "Maintainer": "Wei Wang <periwinkle.david@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "Rfastp_1.23.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/db63858955191364f0826c5f438e88c94ad1b447f7f45210905dd0531869e2c9",
  "_filesize": 2683751,
  "_sha256": "db63858955191364f0826c5f438e88c94ad1b447f7f45210905dd0531869e2c9",
  "_expires": "2027-01-17T14:17:07.000Z",
  "_created": "2026-10-09T14:09:25.000Z",
  "_published": "2026-10-09T14:17:09.399Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 7
  },
  "_upstream": "https://github.com/bioc/Rfastp",
  "_commit": {
    "id": "e419718a583a352c9456d9b7918fdd3a66e639ce",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381582
  },
  "_maintainer": {
    "name": "Wei Wang",
    "email": "periwinkle.david@gmail.com",
    "login": "cafeblue",
    "orcid": "0000-0002-3216-7118",
    "description": "Bioinformatics Specialist",
    "uuid": 2125066
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113859294261,
      "time": 174,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11622375954"
    },
    {
      "job": 113859294298,
      "time": 174,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11622875593"
    },
    {
      "job": 113859294434,
      "time": 275,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11623050783"
    },
    {
      "job": 113859294227,
      "time": 188,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11622785638"
    },
    {
      "job": 113859294405,
      "time": 230,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11622940742"
    },
    {
      "job": 113859294387,
      "time": 160,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11622755552"
    },
    {
      "job": 113859294257,
      "time": 240,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11622346261"
    },
    {
      "job": 113859294345,
      "time": 148,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11622135905"
    },
    {
      "job": 113859294228,
      "time": 313,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11622206220"
    },
    {
      "job": 113856964876,
      "time": 326,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11622680159"
    },
    {
      "job": 113859294117,
      "time": 225,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11623065595"
    },
    {
      "job": 113859294503,
      "time": 361,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11622101445"
    },
    {
      "job": 113859294371,
      "time": 181,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11622845527"
    },
    {
      "job": 113859294391,
      "time": 131,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11622435817"
    },
    {
      "job": 113859294270,
      "time": 290,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11622111231"
    },
    {
      "job": 113859294317,
      "time": 190,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11622865588"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rhtslib",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "rjson",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "qualitycontrol",
    "sequencing",
    "preprocessing",
    "software",
    "zlib",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 572,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Rfastp"
  },
  "_searchresults": 62,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/Rfastp.html",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "catfastq",
    "curvePlot",
    "qcSummary",
    "rfastp",
    "trimSummary"
  ],
  "_help": [
    {
      "page": "catfastq",
      "title": "Concatenate Fastq Files.",
      "topics": [
        "catfastq"
      ]
    },
    {
      "page": "curvePlot",
      "title": "Plot of Base Quality and GC Content.",
      "topics": [
        "curvePlot"
      ]
    },
    {
      "page": "qcSummary",
      "title": "Summary of Fastq Quality Control",
      "topics": [
        "qcSummary"
      ]
    },
    {
      "page": "rfastp",
      "title": "R wrap of fastp",
      "topics": [
        "rfastp"
      ]
    },
    {
      "page": "trimSummary",
      "title": "Summary of Fastq adapter and low quality trimming",
      "topics": [
        "trimSummary"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "Rhtslib",
    "rjson",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg+really1.3.1-1ubuntu3.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Rfastp.Rmd",
      "filename": "Rfastp.html",
      "title": "An Ultra-Fast All-in-One FASTQ preprocessor",
      "author": "Wei Wang periwinkle.david@gmail.com",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "FastQ Quality Control with rfastp",
        "a normal QC run for single-end fastq file.",
        "a normal QC run for paired-end fastq files.",
        "merge paired-end fastq files after QC.",
        "UMI processing",
        "a normal UMI processing for 10X Single-Cell library.",
        "Set a customized UMI prefix and location in sequence name.",
        "A QC example with customized cutoffs and adapter sequence.",
        "multiple input files for read1/2 in a vector.",
        "concatenate multiple fastq files.",
        "catfastq concatenate all the input files into a new file.",
        "Generate report tables/plots",
        "A data frame for the summary.",
        "a ggplot2 object of base quality plot.",
        "a ggplot2 object of GC Content plot.",
        "a data frame for the trimming summary.",
        "Miscellaneous helper functions",
        "Acknowledgments",
        "Session info",
        "References"
      ],
      "created": "2020-06-18 23:17:23",
      "modified": "2020-10-01 22:51:44",
      "commits": 19
    }
  ],
  "_score": 4.491361693834273,
  "_indexed": true,
  "_nocasepkg": "rfastp",
  "_universes": [
    "bioc",
    "cafeblue"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:31.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/6d7639d9b701f24643c32749508002af93c1fc49f90c9cd1f19f9e189fe59c4f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-10-09T14:13:51.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/98944289e798d4f2f7616d9fadf87c51c4e5d9580aeb9c33c6c42b6ed38a3350",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:43.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/5c2878ebc6a7fc34ef6013b9e5a041e23c549a91bd0b699749c75f6c3e225f76",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-10-09T14:13:27.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/57e70bcda9eb7d3948c6f61b1c3cca877b18197b0c101acd58233531cae34af2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:12.000Z",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/6d7cc369435539fc7ad5fc1665fc1a5da4bc78aa8ce9dc87827237eaa7cf7acf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:47.000Z",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/5ec577bf60610e40dcefc9b78c5c259bb53d225b5690638d4757498bc5309d8c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:03.000Z",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/03fe614590ed031a3bab575cadc5942bf2dbd593a8676d9de799d0b4ad05a8b8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-10-09T14:13:30.000Z",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/99a65a2eed58f4e60d10c021eab1776819c480cff712b6163c1ef36cb5967eae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-10-09T14:12:16.000Z",
      "arch": "emscripten",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/9b43af261fe3862e9d8ecee4631edb7fb8ea5c6cde91febe1b0ccb1778793745",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-10-09T14:14:11.000Z",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/9b05b62d24dfe94d3cf90747f85067203c4f7f555c167ff034e912f91cdd7d51",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-10-09T14:11:42.000Z",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/027abcc32389bd768a5a00a35a5d2a641d33fd28fd7568f9ccb6d7962664df22",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-10-09T14:11:27.000Z",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/c421580db4403d2c8b18c8892a3e26afdc1bdb1f734502993d1ac5f32a1ed03e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-10-09T14:13:15.000Z",
      "arch": "aarch64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/7cf8e2625a06cda1442bed87a35f9a6efab5e399bba48fe221094115e3736f37",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-10-09T14:11:46.000Z",
      "arch": "x86_64",
      "commit": "e419718a583a352c9456d9b7918fdd3a66e639ce",
      "fileid": "https://r2.ropensci.org/2f4e4e7819af6633f0ac1dc83a7540c51136ac00f7064ae011d7eb5f9855eba0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37941515645"
    }
  ]
}