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ssw  

Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD
View on CRAN: Click here


Download and install ssw package within the R console
Install from CRAN:
install.packages("ssw")

Install from Github:
library("remotes")
install_github("cran/ssw")

Install by package version:
library("remotes")
install_version("ssw", "0.2.1")



Attach the package and use:
library("ssw")
Maintained by
Nan Xiao
[Scholar Profile | Author Map]
First Published: 2024-09-05
Latest Update: 2024-09-05
Description:
Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast C/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/C++ implementation.
How to cite:
Nan Xiao (2024). ssw: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD. R package version 0.2.1, https://cran.r-project.org/web/packages/ssw. Accessed 18 Feb. 2025.
Previous versions and publish date:
0.2.0 (2024-09-05 18:30)
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