Blog post
CRISPR Guide RNA Design Tool
Benchling’s CRISPR Guide RNA design tool streamlines every step — from scoring and selection to annotation and plasmid assembly — so you can move faster and design with confidence.
Design CRISPR guides with precision, efficiency, and confidence
Batch design
Need to design hundreds of guides at once? Benchling eliminates tedious work by batching gRNA design with automated annotations, up to 100x faster than leading competitors.
On and off target scores
Get on and off-target scores in seconds to optimize for higher activity and minimize off-target effects, reducing trial-and-error for more reliable results.
Plasmid assembly
Save, organize, and link guides to relevant sequences, then seamlessly assemble gRNAs into plasmids for downstream experiments.
Accelerate discovery with an integrated CRISPR toolkit
Speed up design
Import your target gene region, fully annotated
Specify the coordinates, and Benchling will automatically annotate it with everything you need to design guides.
Speed up guide design with automatic exon and CDS annotations
Import directly from 160+ reference genomes
Upload your own sequences in any common file type
Score guide RNA
Score your gRNAs by specificity and efficiency
Use our advanced algorithms to evaluate guides, helping you achieve on-target activity with minimized off-target effects.
Instantly assess off-target and on-target scores
Browse your sequence while reviewing guide performance
Identify the best guides in key domains of a gene
Manage sequences
Save and export guide sequences with ease
Save, organize, and use your guides anywhere. Keep everything connected in Benchling or export them for flexibility.
Save guides as oligos and clone into CRISPR plasmids
Organize with tags and folders for easy retrieval
Export guides with scores and off-target sites for use elsewhere
