genoaligner: GPU-Portable Pairwise Sequence Alignment (WFA + Smith-Waterman)

Pairwise sequence alignment from one portable C++17 core: edit-distance (Levenshtein / WFA-equivalent) and Smith-Waterman local alignment, both with score and CIGAR reconstruction. The core builds and runs anywhere (it is the CPU backend, so it needs no GPU toolchain); the wavefront/GPU backend (ROCm/CUDA) computes the same results with acceleration and is tracked in the sibling C++ repository. A batch API aligns many pairs in one call and reports how many were resolved, so silent under-serving is impossible. Designed to slot into data.frame/tibble pipelines.

Version:	1.0.0
Depends:	R (≥ 4.1.0)
Imports:	Rcpp
LinkingTo:	Rcpp
Suggests:	testthat (≥ 3.0.0), knitr, rmarkdown, spelling
Published:	2026-09-24
DOI:	10.32614/CRAN.package.genoaligner (may not be active yet)
Author:	Angel Robles-Fernandez [aut, cre]
Maintainer:	Angel Robles-Fernandez <a.l.robles.fernandez at gmail.com>
BugReports:	https://github.com/alrobles/genoaligner-r/issues
License:	MIT + file LICENSE
Copyright:	see file COPYRIGHTS
URL:	https://github.com/alrobles/genoaligner-r, https://alrobles.github.io/genoaligner-r/
NeedsCompilation:	yes
SystemRequirements:	C++17
Language:	en-US
Materials:	NEWS
CRAN checks:	genoaligner results

Documentation:

Reference manual:

genoaligner.html , genoaligner.pdf

Downloads:

Package source:	genoaligner_1.0.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): genoaligner_1.0.0.tgz, r-release (x86_64): genoaligner_1.0.0.tgz, r-oldrel (x86_64): genoaligner_1.0.0.tgz

Linking:

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