Package: ssw 0.2.0

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]

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ssw.pdf |ssw.html✨
ssw/json (API)
NEWS

Peer review:

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

On CRAN:

bioinformaticsreticulatesequence-alignmentsimdsmith-waterman

6 exports 5 stars 1.39 score 12 dependencies 42 downloads

Last updated 7 days agofrom:ef6b6ff577. Checks:OK: 7. Indexed: yes.

Exports:alignforce_alignformatterinstall_ssw_pyis_installed_ssw_pyssw_py

Dependencies:herejsonlitelatticeMatrixpngrappdirsRcppRcppTOMLreticulaterlangrprojrootwithr