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.


Reference manual

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install.packages("genoaligner")

1.0.0 by Angel Robles-Fernandez, 22 days ago


https://github.com/alrobles/genoaligner-r, https://alrobles.github.io/genoaligner-r/


Report a bug at https://github.com/alrobles/genoaligner-r/issues


Browse source code at https://github.com/cran/genoaligner


Authors: Angel Robles-Fernandez [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports Rcpp

Suggests testthat, knitr, rmarkdown, spelling

Linking to Rcpp

System requirements: C++17


See at CRAN