Aligning sequences with genoaligner

genoaligner aligns sequences: pairs of them with align_edit() and align_sw(), and sets of them with msa_align() and msa_codon(). This vignette covers the two standard pairwise problems; for multiple alignment see vignette("msa-codon-lepus").

align_edit() — edit distance (Levenshtein; the WFA-equivalent score) with an optional CIGAR.
align_sw() — Smith-Waterman local alignment with affine gaps, CIGAR, and the aligned span’s coordinates.

Edit distance

align_edit("ACGTACGT", "ACGTTCGT", smax = 8)
#>   score resolved    cigar rescore_ok wellformed_ok
#> 1     1     TRUE MMMMXMMM       TRUE          TRUE

By default smax = 64: a pair is resolved only when its true equal-cost edit distance is at most smax. If it exceeds the bound the pair comes back resolved = FALSE with an NA score rather than a wrong number — size smax to your data to avoid silently under-serving.

Both functions are vectorised over the pair columns, so they map straight into a pipeline:

pairs <- data.frame(
  query     = c("ACGTACGT", "GGGG",    "TTTTCCCC", "AAAACCCC"),
  reference = c("ACGTTCGT", "ACGT",    "TTTTCGCG", "AAAATTTT")
)
pairs$result <- align_edit(pairs$query, pairs$reference, smax = 8)
pairs
#>      query reference result.score result.resolved result.cigar
#> 1 ACGTACGT  ACGTTCGT            1            TRUE     MMMMXMMM
#> 2     GGGG      ACGT            3            TRUE         XXMX
#> 3 TTTTCCCC  TTTTCGCG            2            TRUE     MMMMMXMX
#> 4 AAAACCCC  AAAATTTT            4            TRUE     MMMMXXXX
#>   result.rescore_ok result.wellformed_ok
#> 1              TRUE                 TRUE
#> 2              TRUE                 TRUE
#> 3              TRUE                 TRUE
#> 4              TRUE                 TRUE

Smith-Waterman local alignment

align_sw("TTTACGTGTT", "ACGTGT", scoring = c(2, -3, 5, 2))
#>   score start_i start_j end_i end_j  cigar rescore_ok wellformed_ok too_large
#> 1    12       3       0     8     5 MMMMMM       TRUE          TRUE     FALSE

scoring is (match, mismatch, gap_open, gap_extend); penalties are positive and subtracted. The result includes the 0-based coordinates of the aligned span and the CIGAR over that span.

The CIGAR convention

Identical for both entry points: M and X consume a text and a pattern base (M on equal, X on differing characters); I consumes an extra text base; D consumes an extra pattern base. Empty inputs and score == 0 (no positive-scoring local alignment) are reported with NA/-1 coordinates.

GPU backend

The workhorse of this package is a self-contained CPU core that needs no GPU toolchain. The wavefront/GPU backend (ROCm and CUDA) computes the same results with acceleration and is tracked in the sibling C++ genoaligner repository.