{
  "_id": "6a1aea011d7bb097a09f2e29",
  "Package": "Rbowtie2",
  "Type": "Package",
  "Title": "An R Wrapper for Bowtie2 and AdapterRemoval",
  "Version": "2.19.0",
  "Date": "2021-10-5",
  "Authors@R": "c(person(given = \"Zheng\", family = \"Wei\", role = c(\"aut\",\"cre\"),\nemail = \"wzweizheng@qq.com\"),\nperson(given = \"Wei\", family = \"Zhang\", role = c(\"aut\"),\nemail = \" weizhang0505@126.com\"))",
  "Description": "This package provides an R wrapper of the popular bowtie2\nsequencing reads aligner and AdapterRemoval, a convenient tool\nfor rapid adapter trimming, identification, and read merging.\nThe package contains wrapper functions that allow for genome\nindexing and alignment to those indexes. The package also\nallows for the creation of .bam files via Rsamtools.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "SystemRequirements": "C++11, GNU make, samtools",
  "Archs": "x64",
  "RoxygenNote": "7.1.1",
  "biocViews": "Sequencing, Alignment, Preprocessing",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:19 UTC",
  "RemoteUrl": "https://github.com/bioc/Rbowtie2",
  "RemoteRef": "HEAD",
  "RemoteSha": "8a7676d920fac4355704da398d80918064172273",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 09:35:40 UTC",
    "User": "root"
  },
  "Author": "Zheng Wei [aut, cre],\nWei Zhang [aut]",
  "Maintainer": "Zheng Wei <wzweizheng@qq.com>",
  "MD5sum": "9a7f798f794ed72a6ed6cb347bb8450a",
  "_user": "bioc",
  "_type": "src",
  "_file": "Rbowtie2_2.19.0.tar.gz",
  "_fileid": "14ad79c580cbdce74092a9c0f67db3297700072eb30ecbc2150289a06baccdba",
  "_filesize": 1719855,
  "_sha256": "14ad79c580cbdce74092a9c0f67db3297700072eb30ecbc2150289a06baccdba",
  "_created": "2026-05-30T09:35:40.000Z",
  "_published": "2026-05-30T13:45:37.753Z",
  "_jobs": [
    {
      "job": 78640192114,
      "time": 347,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307369526"
    },
    {
      "job": 78640192156,
      "time": 352,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307277420"
    },
    {
      "job": 78640192133,
      "time": 690,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307401868"
    },
    {
      "job": 78640192145,
      "time": 367,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307278550"
    },
    {
      "job": 78640192134,
      "time": 400,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307375273"
    },
    {
      "job": 78640192155,
      "time": 226,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308613557"
    },
    {
      "job": 78640192160,
      "time": 350,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307300241"
    },
    {
      "job": 78640192154,
      "time": 224,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308614492"
    },
    {
      "job": 78640192153,
      "time": 489,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307312764"
    },
    {
      "job": 78639265947,
      "time": 605,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307239518"
    },
    {
      "job": 78640192122,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78640192131,
      "time": 383,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307374475"
    },
    {
      "job": 78640192152,
      "time": 327,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307369260"
    },
    {
      "job": 78640192126,
      "time": 362,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307372666"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Rbowtie2",
  "_commit": {
    "id": "8a7676d920fac4355704da398d80918064172273",
    "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": 1777380379
  },
  "_maintainer": {
    "name": "Zheng Wei",
    "email": "wzweizheng@qq.com",
    "login": "wzthu",
    "description": "eXplainable AI (XAI) |\ndeep learning |\ngenomics |\ncomputational biology |\nbioinformatics ",
    "uuid": 19941845
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "alignment",
    "preprocessing",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 764,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Rbowtie2"
  },
  "_searchresults": 31,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Rbowtie2.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adapterremoval_usage",
    "adapterremoval_version",
    "bowtie2",
    "bowtie2_build",
    "bowtie2_build_usage",
    "bowtie2_samtools",
    "bowtie2_usage",
    "bowtie2_version",
    "identify_adapters",
    "remove_adapters"
  ],
  "_help": [
    {
      "page": "dot-callbinary",
      "title": "Make system call for binaries",
      "topics": [
        ".callbinary"
      ]
    },
    {
      "page": "adapterremoval_usage",
      "title": "Print available arguments for adapterremoval",
      "topics": [
        "adapterremoval_usage"
      ]
    },
    {
      "page": "adapterremoval_version",
      "title": "Print version information of adapterremoval",
      "topics": [
        "adapterremoval_version"
      ]
    },
    {
      "page": "bowtie2",
      "title": "Interface to bowtie2 of bowtie2-2.2.3",
      "topics": [
        "bowtie2"
      ]
    },
    {
      "page": "bowtie2_build_usage",
      "title": "Print available arguments that can be passed to bowtie2_build()",
      "topics": [
        "bowtie2_build_usage"
      ]
    },
    {
      "page": "bowtie2_samtools",
      "title": "Interface to bowtie2-2.4.4 align function",
      "topics": [
        "bowtie2_samtools"
      ]
    },
    {
      "page": "bowtie2_usage",
      "title": "Print available arguments that can be passed to bowtie2()",
      "topics": [
        "bowtie2_usage"
      ]
    },
    {
      "page": "bowtie2_version",
      "title": "Print version information of bowtie2-2.4.4",
      "topics": [
        "bowtie2_version"
      ]
    },
    {
      "page": "bowtie2-build",
      "title": "Interface to bowtie2-2.4.4 build function",
      "topics": [
        "bowtie2-build",
        "bowtie2_build"
      ]
    },
    {
      "page": "checkFileCreateable",
      "title": "Check if file is creatable",
      "topics": [
        "checkFileCreatable",
        "checkFileCreateable"
      ]
    },
    {
      "page": "checkFileExist",
      "title": "Check if file exists",
      "topics": [
        "checkFileExist"
      ]
    },
    {
      "page": "checkIndexType",
      "title": "Determine bowtie2 index type",
      "topics": [
        "checkIndexType"
      ]
    },
    {
      "page": "checkPathExist",
      "title": "Check if path exists",
      "topics": [
        "checkPathExist"
      ]
    },
    {
      "page": "checkSamtoolsExists",
      "title": "Check if samtools exists on the system",
      "topics": [
        "checkSamtoolsExists"
      ]
    },
    {
      "page": "identify_adapters",
      "title": "identify adapters for paired-end reads",
      "topics": [
        "identify_adapters"
      ]
    },
    {
      "page": "remove_adapters",
      "title": "Interface to bowtie2 of adapterremoval-2.2.1a",
      "topics": [
        "remove_adapters"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Rbowtie2/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "codetools",
    "cpp11",
    "crayon",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lambda.r",
    "magrittr",
    "Rhtslib",
    "Rsamtools",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Rbowtie2-Introduction.Rmd",
      "filename": "Rbowtie2-Introduction.html",
      "title": "An Introduction to Rbowtie2",
      "author": "Zheng Wei and Wei Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "An Example Workflow by Using Rbowtie2",
        "Installation",
        "Loading",
        "AdapterRemoval",
        "Idetitify Adapter",
        "Remove Adapter",
        "Additional Arguments and Version",
        "Bowtie2",
        "Build Bowtie2 Index",
        "Additional Arguments of Bowtie Build",
        "Bowtie2 Alignment",
        "Additional Arguments and Version of Bowtie2 Aligner",
        "Session Infomation",
        "Acknowledgement",
        "References"
      ],
      "created": "2017-08-23 06:37:21",
      "modified": "2021-09-18 11:52:45",
      "commits": 22
    }
  ],
  "_score": 5.445604203273597,
  "_indexed": true,
  "_nocasepkg": "rbowtie2",
  "_universes": [
    "bioc",
    "wzthu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-30T09:41:39.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "8be5cb97e7413cd57ad5485f67c0cb99048cf3deb1158f40b3daf9916300ee49",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-30T09:58:33.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "ff17352b968c6a4f47fc4d5034b2b767e3016032a31196e1f19958ef7b6fa04b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-30T09:41:37.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "7e09c066c105f8c2394c614f89b4fe261f793fac3c196463eec89b6351f011c0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-30T09:58:35.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "6d9f6ee2d24feb1eea5ea25a3749e094be40080abcebcc5506700b909cf706d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-30T13:42:58.000Z",
      "arch": "aarch64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "a863c4641c04a89e0407153808c2dfdd6ce591270b7435a04cbbdac5cea6cb64",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-30T09:45:20.000Z",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "7e490076f1aff9ff5c4c5e7296620794e2ebb12737eb2402b5669888fe5925e0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-30T13:43:00.000Z",
      "arch": "aarch64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "466af5f207d3f3c00ae8f47fa159b65766e526747366ca7174d113902c6131e3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-30T09:46:20.000Z",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "3bf8d6a92208bb5c3f8d0c65b08efa2fc6300b81a2d70e7adfda74300b1aed11",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-30T09:57:06.000Z",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "3be5b4705081ac5ddb98ef9e4f8c65c5f858fa3bb66954b2b6ce54406d174221",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-30T09:56:56.000Z",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "90ff7bedfa82ba5bd04aae7d55be93cf58a6a0b6229ee547a9632c20f2c5dd69",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-30T09:57:04.000Z",
      "arch": "x86_64",
      "commit": "8a7676d920fac4355704da398d80918064172273",
      "fileid": "351b388714014cd55081408ce8adc85369ce8aa0a0fccdb0618026465d773de5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675607776"
    }
  ]
}