genoaligner: GPU-portable pairwise sequence alignment

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 sibling C++ library tracks the GPU (ROCm/CUDA) backend that computes the same results with wavefront acceleration.

Details

The two entry points are align (edit distance bounded by smax) and align_sw (local Smith-Waterman with affine gaps). Both are vectorised over pairs, so a two-column pipeline (query, reference) maps straight to a data.frame of scores and CIGARs.

See also

Useful links:

• https://github.com/alrobles/genoaligner-r

• https://alrobles.github.io/genoaligner-r/

• Report bugs at https://github.com/alrobles/genoaligner-r/issues

Author

Maintainer: Angel Robles-Fernandez a.l.robles.fernandez@gmail.com

Authors:

• Angel Robles-Fernandez a.l.robles.fernandez@gmail.com