On-target scoring

On-target scorers predict cleavage activity. RuleSet3 is the default (--tracr); the deep models are added with --cas9_scorer (SpCas9) or --cas12a_scorer (Cas12a). Each adds one column; --min_<scorer> drops low guides before the off-target pass.

RuleSet3

--tracr Hsu2013 | Chen2013 | both – SpCas9 (default). Output is a z-score; the two values are tracrRNA variants. DeWeirdt et al. 2022 (the rs3 package).

DeepSpCas9

--cas9_scorer deepspcas9 – SpCas9, CNN on-target activity. Kim et al. 2019, Sci. Adv.

DeepHF

--cas9_scorer deephf_wt_u6 | deephf_esp | deephf_hf – SpCas9 (wildtype/U6, eSpCas9-1.1, SpCas9-HF1); BiLSTM + biofeatures. Wang et al. 2019, Nat. Commun.

DeepCpf1

--cas12a_scorer deepcpf1 – Cas12a (AsCas12a / LbCas12a), the original seq-DeepCpf1 CNN. Kim et al. 2018, Nat. Biotechnol.

enPAM+GB

--cas12a_scorer enpam_gb – enAsCas12a; gradient-boosted on RuleSet2 features. DeWeirdt et al. 2021, Nat. Biotechnol.

enseq-DeepCpf1

--cas12a_scorer enseq_deepcpf1 – Cas12a (modern AsCas12a), sequence-only CNN. Chen et al. 2025, Nat. Commun.

seq-DeepCpf1variants

--cas12a_scorer seq_deepcpf1variants --cas12a_variant <name> – per-variant CNNs for 23 Cas12a variants: AsCas12a, AsCas12a_Ultra (2xNLS), enAsCas12a-HF1, HyperFi-AsCas12a, and the LbCas12a / FnCas12a / iCas12a / Lb2Cas12a / Eb / Ce families. Names are case- and separator-insensitive. Chen et al. 2025, Nat. Commun.