The UCSC Cas12a track pipeline

Four steps take a genome FASTA to a browser-ready track:

  1. Setup the environment, the GPU engine binary, and the UCSC tools.

  2. Index + guides build the off-target index (PAM TTTN) and enumerate every TTTV protospacer.

  3. Score + assemble run the one score_guides --ucscgb command: on-target + off-target scoring, internally chunked and fanned across GPUs, merged into one track.

  4. Outputs inspect the three files the build produces.