CRISPRware

CRISPRware identifies, scores, and ranks CRISPR guide RNAs (gRNAs) from a genome, with optional NGS-guided targeting (RNA-seq, Ribo-seq, ATAC-seq, ChIP-seq). On-target activity is predicted by a suite of deep-learning models for SpCas9 and Cas12a; off-target specificity is scored by the in-tree Rust scanner crispr-ots (or Guidescan2).

Pipeline

        flowchart LR
    A["<b>preprocess_annotation</b><br/><small>gene models, RNA-seq filter</small>"]
    I["<b>index_genome</b><br/><small>off-target index</small>"]
    G["<b>generate_guides</b><br/><small>find protospacers</small>"]
    S["<b>score_guides</b><br/><small>on-target + off-target</small>"]
    R["<b>rank_guides</b><br/><small>filter + select per target</small>"]
    A --> G --> S --> R
    I --> S
    classDef s fill:#eaf2fb,stroke:#3a6ea5,color:#16314a;
    class A,I,G,S,R s;

Each step is a crisprware <module> subcommand; chain them or run any in isolation. The pages below walk each module with a runnable example on the bundled C. elegans chrIII test data.

Getting started

Modules

Scoring

Scoring methods

Cas12a UCSC tracks

Reference