| moi | No | multiplicity of infection, 0 to leave it unplanned. Joung et al. 2017 recommends <0.3 so most cells take at most one perturbation; reported, never applied. Advanced. | |
| rank | No | which on-target score orders the candidates. A guide the chosen model cannot score is left unranked, never dropped. Rule Set 3 is deliberately not offered here: its weights are a 9.8 MB download the editor fetches on demand, and this engine is headless and cannot fetch — offering it would return an unranked pool that looked ranked. | ruleSet1 |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| nuclease | No | the nuclease (PAM + spacer length) to scan for. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')). | SpCas9 |
| barcode_id | No | CRISPOR subpool barcode id, 0 for none — lets several sub-libraries share one synthesis array and amplify apart. Advanced. | |
| target_type | No | annotation type to take as the targets, one pool entry per feature of that type (`CDS`, `gene`, …). Leave unset to treat the whole record as a single target — which is what a saturating-mutagenesis pool over one locus wants. | |
| exclude_graf | No | drop guides matching a Graf 2019 inactive motif (the TT/GCC classes). | |
| custom_prefix | No | your vector's 5' cloning overhang. BOTH sides must be given, or the pool stays on pLentiGuide — that is upstream's rule, reproduced. Advanced. | |
| custom_suffix | No | your vector's 3' cloning overhang. Advanced. | |
| exclude_poly_t | No | drop guides whose spacer carries a Pol-III (TTTT) terminator. | |
| representation | No | cells you intend to keep carrying EACH guide. Joung et al. 2017 recommends >500; the default here is the neutral 1, not that recommendation, so the plan is the identity until you choose a scale. Advanced. | |
| reads_per_oligo | No | sequencing reads per guide in the readout. Joung et al. 2017 recommends >500 for a screen (>100 to QC the cloned library); the default here is the neutral 1. Advanced. | |
| guides_per_target | No | how many guides to take per target, best-ranked first. | |
| restriction_enzymes | No | cloning enzymes whose recognition site must NOT appear in the spacer — a hit drops the guide from the pool. Advanced. | |
| transduction_efficiency | No | fraction of cells that take up a construct, 0-1 — sizes the transduction back up from the cells you need to keep. Advanced. | |