crispr-library-design

Design pooled CRISPR sgRNA libraries and generate oligo orders.

64|12|Updated Apr 7, 2026

Search Tags:#ensembl #library-design #crispr #off-target #sgrna-design #gene-targeting #oligo-synthesis

Ready to run

npx skills add https://github.com/MDhewei/bioinfor-claw --skill crispr-library-design

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: crispr-library-design
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/crispr-design-and-analysis/crispr-library-design
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill crispr-library-design

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, numpy, pandas, matplotlib, and includes scripts (resource) components.

What problem does it solve?

This skill automates the design of pooled CRISPR sgRNA libraries, selecting top guides per gene and generating oligo orders for synthesis, streamlining library creation for large-scale screens.

Core Features & Use Cases

Design sgRNA guides for each target gene using PAM constraints and GC filters, with per-gene ranking.
Apply efficiency and off-target scoring to identify top guides and ensure library quality.
Generate non-targeting controls and output ready-to-synthesize oligo sequences, plus summary statistics and plots.
Supports vector design with optional flanking sequences and multiple output formats (TSV/CSV/FASTA).

Quick Start

Run the design script with a comma-separated list of gene symbols to produce a ready-to-synthesize CRISPR sgRNA library for your targets.

Frequently Asked Questions about crispr-library-design

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I design a pooled CRISPR sgRNA library for a list of target genes?▼

To design a pooled CRISPR sgRNA library, input a comma-separated list of gene symbols along with desired guides per gene, controls, and PAM constraints. The tool selects top guides, generates non-targeting controls, and outputs ready-to-synthesize oligo sequences in TSV, CSV, or FASTA formats.

What's the best way to generate oligo synthesis orders for CRISPR screens?▼

Generating oligo synthesis orders for CRISPR screens involves applying efficiency and off-target scoring to rank sgRNA guides per gene. This skill outputs vector-ready sequences with optional flanking regions, producing TSV, CSV, and FASTA files plus summary plots for direct synthesis.

Does CRISPR library design support both human and mouse genomes?▼

CRISPR library design supports both human and mouse genomes for target gene screening. You can input gene symbols from either species, apply PAM constraints and GC filters, and generate enrichment libraries with non-targeting controls and vector-ready outputs.

Can I include non-targeting controls in my sgRNA library design?▼

Yes, you can include non-targeting controls in your sgRNA library design by specifying the number of controls needed in the input parameters. The tool automatically generates these controls alongside top-ranked guides for your target genes.

How are sgRNA guides ranked and selected for off-target effects?▼

sgRNA guides are ranked and selected by applying efficiency scoring and off-target analysis to ensure library quality. The process uses PAM constraints and GC filters to identify top guides per gene for your pooled CRISPR library.

What output formats are available for synthesized CRISPR oligo sequences?▼

Available output formats for synthesized CRISPR oligo sequences include TSV, CSV, and FASTA. The design process also generates summary statistics and plots to visualize library quality alongside the vector-ready sequence files.