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) <doi:10.1371/journal.pone.0082138> 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
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2024-09-18 00:26:03 UTC; nanx
Author: Nan Xiao [aut, cre, cph] (<https://orcid.org/0000-0002-0250-5673>)
Maintainer: Nan Xiao <me@nanx.me>
Repository: CRAN
Date/Publication: 2024-09-18 02:10:02 UTC
Built: R 4.6.0; ; 2026-04-27 20:30:35 UTC; unix
