index_genome

Build the crispr-ots off-target index that score_guides scans against (fast, exact-mismatch).

crisprware index_genome -f tests/test_data/ce11/chrIII_sequence.fasta -p NGG -l 20

chrIII_sequence_crisprots/
  chrIII_sequence_crisprots.crot      # the crispr-ots mmap off-target database

The index is PAM- and length-aware, so -p/--pam and -l/--protospacer_length are required and must match the guides you will score (NGG/20 for SpCas9, TTTN/23 --pam_5_prime for Cas12a).

Options you reach for

• --pam_5_prime – PAM is 5’ of the protospacer (Cas12a).

• --bin_width – crispr-ots index bin size (memory/throughput tradeoff).

• --locations_to_keep <bed/gtf> [--feature CDS] [-w up down] – index only these regions (plus an optional flanking window) instead of the whole FASTA, for tighter, faster specificity.

Tip

For Cas12a use -p TTTN -l 23 --pam_5_prime (index TTTN so weak-PAM off-targets are still found). Guidescan2 ships prebuilt indices for some genomes at https://guidescan.com/downloads.