Package: ssw 0.2.1

ssw: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD

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.

Authors:Nan Xiao [aut, cre, cph]

ssw_0.2.1.tar.gz
ssw_0.2.1.zip(r-4.5)ssw_0.2.1.zip(r-4.4)ssw_0.2.1.zip(r-4.3)
ssw_0.2.1.tgz(r-4.5-any)ssw_0.2.1.tgz(r-4.4-any)ssw_0.2.1.tgz(r-4.3-any)
ssw_0.2.1.tar.gz(r-4.5-noble)ssw_0.2.1.tar.gz(r-4.4-noble)
ssw_0.2.1.tgz(r-4.4-emscripten)ssw_0.2.1.tgz(r-4.3-emscripten)
ssw.pdf |ssw.html
ssw/json (API)
NEWS

# Install 'ssw' in R:
install.packages('ssw', repos = c('https://nanxstats.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nanxstats/ssw-r/issues

Pkgdown site:https://nanx.me

On CRAN:

Conda:

bioinformaticsreticulatesequence-alignmentsimdsmith-waterman

5.18 score 6 stars 460 downloads 6 exports 12 dependencies

Last updated 6 months agofrom:9b36eb0fcb. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 16 2025
R-4.5-winOKMar 16 2025
R-4.5-macOKMar 16 2025
R-4.5-linuxOKMar 16 2025
R-4.4-winOKMar 16 2025
R-4.4-macOKMar 16 2025
R-4.4-linuxOKMar 16 2025
R-4.3-winOKMar 16 2025
R-4.3-macOKMar 16 2025

Exports:alignforce_alignformatterinstall_ssw_pyis_installed_ssw_pyssw_py

Dependencies:herejsonlitelatticeMatrixpngrappdirsRcppRcppTOMLreticulaterlangrprojrootwithr

Getting started with ssw-r: Sequence alignment examples

Rendered fromssw.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2024-09-10
Started: 2020-06-07