Package: ssw Title: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD Version: 0.2.1 Authors@R: c( person("Nan", "Xiao", email = "me@nanx.me", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-0250-5673")) ) Description: Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast 'C' and 'C++' implementation of the Smith-Waterman algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning alignment information and suboptimal alignment scores. The core 'SSW' library offers performance improvements for various bioinformatics tasks, including protein database searches, short-read alignments, primary and split-read mapping, structural variant detection, and read-overlap graph generation. These features make 'SSW' particularly useful for genomic applications. Zhao et al. (2013) developed the original 'C' and '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 installation instructions can be found in the README file. VignetteBuilder: knitr Depends: R (>= 4.1.0) Imports: reticulate Suggests: knitr, rmarkdown 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: 2026-06-17 08:55:04 UTC; root Author: Nan Xiao [aut, cre, cph] (ORCID: ) Maintainer: Nan Xiao