{ "_id": "6a3261c03efcd9bda438464b", "Package": "ssw", "Title": "Striped Smith-Waterman Algorithm for Sequence Alignment using\nSIMD", "Version": "0.2.1", "Authors@R": "c(\nperson(\"Nan\", \"Xiao\", email = \"me@nanx.me\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-0250-5673\"))\n)", "Description": "Provides an R interface for 'SSW' (Striped Smith-Waterman)\nvia its 'Python' binding 'ssw-py'. 'SSW' is a fast 'C' and\n'C++' implementation of the Smith-Waterman algorithm for\npairwise sequence alignment using\nSingle-Instruction-Multiple-Data (SIMD) instructions. 'SSW'\nenhances the standard algorithm by efficiently returning\nalignment information and suboptimal alignment scores. The core\n'SSW' library offers performance improvements for various\nbioinformatics tasks, including protein database searches,\nshort-read alignments, primary and split-read mapping,\nstructural variant detection, and read-overlap graph\ngeneration. These features make 'SSW' particularly useful for\ngenomic applications. Zhao et al. (2013)\n developed the original 'C'\nand 'C++' implementation.", "License": "MIT + file LICENSE", "URL": "https://nanx.me/ssw-r/, https://github.com/nanxstats/ssw-r", "BugReports": "https://github.com/nanxstats/ssw-r/issues", "Encoding": "UTF-8", "SystemRequirements": "Python (>= 3.6.0), ssw-py (>= 1.0.0). Detailed\ninstallation instructions can be found in the README file.", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libpng-dev python3", "Repository": "https://nanxstats.r-universe.dev", "Date/Publication": "2024-09-17 22:19:48 UTC", "RemoteUrl": "https://github.com/nanxstats/ssw-r", "RemoteRef": "HEAD", "RemoteSha": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-17 08:55:04 UTC", "User": "root" }, "Author": "Nan Xiao [aut, cre, cph] (ORCID:\n)", "Maintainer": "Nan Xiao ", "MD5sum": "a283e9183b33e294d5d1b8166bd85778", "_user": "nanxstats", "_type": "src", "_file": "ssw_0.2.1.tar.gz", "_fileid": "050026f72f1f77e65bc34e17a566482c4327ba2234e7071c1b2af5c5fb9d755a", "_filesize": 151180, "_sha256": "050026f72f1f77e65bc34e17a566482c4327ba2234e7071c1b2af5c5fb9d755a", "_created": "2026-06-17T08:55:04.000Z", "_published": "2026-06-17T08:58:40.405Z", "_distro": "noble", "_jobs": [ { "job": 81856295869, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7690609542" }, { "job": 81856295802, "time": 176, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7690616960" }, { "job": 81856295822, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7690598925" }, { "job": 81856295919, "time": 96, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7690588072" }, { "job": 81855818809, "time": 149, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7690551583" }, { "job": 81856295864, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7690589751" }, { "job": 81856295996, "time": 98, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7690589978" }, { "job": 81856295987, "time": 103, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7690592020" }, { "job": 81856295896, "time": 123, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7690598083" } ], "_buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nanxstats/ssw-r", "_commit": { "id": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "author": "Nan Xiao ", "committer": "GitHub ", "message": "Merge pull request #24 from nanxstats/news\n\nUpdate news for v0.2.1", "time": 1726611588 }, "_maintainer": { "name": "Nan Xiao", "email": "me@nanx.me", "login": "nanxstats", "bluesky": "@nanxstats.bsky.social", "linkedin": "in/nanxstats", "twitter": "@nanxstats", "description": "Senior Principal DSX Data Scientist @Genentech. Prev principal biostatistician @Merck, senior genomic data scientist @sbg.", "uuid": 199363, "orcid": "0000-0002-0250-5673" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "reticulate", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "nanxstats", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "bioinformatics", "reticulate", "sequence-alignment", "simd", "smith-waterman" ], "_stars": 6, "_contributors": [ { "user": "nanxstats", "count": 53, "uuid": 199363 } ], "_userbio": { "uuid": 199363, "type": "user", "name": "Nan Xiao", "followers": 805, "description": "Senior Principal DSX Data Scientist @Genentech. Prev principal biostatistician @Merck, senior genomic data scientist @sbg." }, "_downloads": { "count": 561, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ssw" }, "_devurl": "https://github.com/nanxstats/ssw-r", "_pkgdown": "https://nanx.me/ssw-r/", "_searchresults": 0, "_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/readme.html", "extra/readme.md", "extra/ssw.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/nanxstats/ssw-r", "_realowner": "nanxstats", "_cranurl": true, "_releases": [ { "version": "0.2.0", "date": "2024-09-05" }, { "version": "0.2.1", "date": "2024-09-18" } ], "_exports": [ "align", "force_align", "formatter", "install_ssw_py", "is_installed_ssw_py", "ssw_py" ], "_help": [ { "page": "align", "title": "Perform Smith-Waterman alignment of a read against a reference sequence", "topics": [ "align" ] }, { "page": "force_align", "title": "Perform forced alignment with increased gap open penalty", "topics": [ "force_align" ] }, { "page": "formatter", "title": "Format and pretty-print SSW forced alignment results without truncation", "topics": [ "formatter" ] }, { "page": "install_ssw_py", "title": "Install ssw-py and its dependencies", "topics": [ "install_ssw_py" ] }, { "page": "is_installed_ssw_py", "title": "Is ssw-py installed?", "topics": [ "is_installed_ssw_py" ] }, { "page": "print.ssw", "title": "Print SSW alignment results", "topics": [ "print.ssw" ] }, { "page": "ssw_py", "title": "Global reference to ssw-py", "topics": [ "ssw_py" ] } ], "_pkglogo": "https://github.com/nanxstats/ssw-r/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/nanxstats/ssw-r/raw/HEAD/README.md", "_rundeps": [ "here", "jsonlite", "lattice", "Matrix", "png", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "withr" ], "_vignettes": [ { "source": "ssw.Rmd", "filename": "ssw.html", "title": "Getting started with ssw-r: Sequence alignment examples", "engine": "knitr::rmarkdown", "headings": [ "Exact alignment", "Deletion", "Insertion with gap open", "Insertion with no gap open penalty", "Specify start index", "Forced alignment", "Acknowledgements", "References" ], "created": "2020-06-07 02:08:34", "modified": "2024-09-10 02:41:53", "commits": 11 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "ssw", "_universes": [ "nanxstats" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.1", "date": "2026-06-17T08:57:25.000Z", "distro": "noble", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "d487b5001bafe80b412906cf27e04299cb52c9c14820cde4346b1e5c03e2c967", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.6.0", "os": "linux", "version": "0.2.1", "date": "2026-06-17T08:57:46.000Z", "distro": "noble", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "4eede4e9a23d012b80eef72cbf0e7fd40140a84f7728c20834f8fdc6329b3e56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.5.3", "os": "mac", "version": "0.2.1", "date": "2026-06-17T08:57:03.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "f9966a8aab3542b952b92cabd33605196359838bf42433592d89c9bd0c1c483a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.6.0", "os": "mac", "version": "0.2.1", "date": "2026-06-17T08:56:35.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "5000c29bd10aa680a0d9562af88fbd1fa1fdf57f3287961b30aaa1dd4c86984b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.1", "date": "2026-06-17T08:57:01.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "b557cf43e0592ee40b4afe636f8e0343302be2329761ad4d358071843f6f286d", "status": "success", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.7.0", "os": "win", "version": "0.2.1", "date": "2026-06-17T08:56:21.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "4e7a3da0f564d2084a7cb00cae336d4e291e85d126e1894a1525813e35f06f68", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.5.3", "os": "win", "version": "0.2.1", "date": "2026-06-17T08:56:34.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "73ccb28c4232ee4be1bfdf071e5b389a3a3f339936e2657fbe19ba7ffa18ec4b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" }, { "r": "4.6.0", "os": "win", "version": "0.2.1", "date": "2026-06-17T08:56:47.000Z", "commit": "9b36eb0fcb17d5027d3aaf33d2f680200414eeb7", "fileid": "be4ad84a35e98cdf8067606b3ac6c74cc230ef82f2b0f7e60f08ac362b73a3ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanxstats/actions/runs/27677301920" } ] }