hspZ: GPU-accelerated HSPs backend

GPU-accelerated HSPs backend

Install Quick start Algorithm

NVIDIA and AMD via ZLUDA · 1–N GPU workers · KegAlign-compatible output

Whole-genome alignment

hspZ replaces Seed + Filter—not LASTZ.

  1. GenomesSoftmasked FASTA, FASTA.gz, or 2bit.
  2. hspZSpaced seeds, X-drop, entropy, deterministic `.segments`.
  3. LASTZGapped extension from accepted HSPs.
  4. ChainConnect collinear local alignments.
  5. NetSelect the hierarchical genome alignment.