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library-design

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Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.

When to use

• Designing pooled sgRNA libraries
• CRISPR knockout library design
• CRISPRi and CRISPRa library design
• Cas12a multiplex library design
• Base-editor and prime-editor screen design
• On-target and off-target guide scoring
• TSS-relative positioning for CRISPRi/a
• Library QC and skew diagnosis

When not to use

• CRISPRi/a targeting wrong TSS
• Cas9 KO of essential paralogs
• Base editor over an exon-intron boundary

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