SPACER

Spacer Profiling and Activity-driven crRNA Efficacy Ranking

Design, score, and rank crRNAs optimized for nucleic acid detection. High-performance guide RNA design for Cas12 and Cas13 diagnostic systems.

Start FindingDocumentation

Everything you need for guide RNA design

From sequence analysis to primer generation — a complete toolkit for CRISPR-based diagnostics, all in one place.

Guide RNA Design
Cas12 (DNA-targeting) and Cas13 (RNA-targeting) with configurable PAM sequences and spacer lengths.

TTTN · TTTV · PFS-free

Activity Prediction
AI-powered activity prediction with EasyDesign (Cas12) and ADAPT (Cas13) models for scoring guide efficacy.

EasyDesign (Cas12) · ADAPT (Cas13)

RNA Secondary Structure
Vienna RNA folding integration for structure-aware guide selection and accessibility scoring.
Primer Design
Primer3 integration for generating flanking primers alongside your diagnostic guides.
Variant Coverage
Evolutionary approach for designing spacers that detect multiple or single variants via ADAPT.
Composite Scoring
0–100 scoring with tier classification, GC analysis, homopolymer detection, and quality flags.

No dependency hell

Scientific dependencies compiled from source into a single distributable. Install once — on any platform — and everything just works.

Zero external dependencies
Primer3 and ViennaRNA are compiled from vendored C source directly into the binary. ONNX Runtime is bundled automatically for ML inference. No system packages to install — no apt-get, brew, or conda.

Primer3 · ViennaRNA · ONNX Runtime

First-class Python support
Install with your favorite package manager and get Rust-native performance in your Python workflows. Pre-built wheels bundle all native dependencies — full speed, zero compilation.

pip · uv · poetry

Use SPACER your way

Web
CLI
TUI
Library
Python

Blazingly fast

Reimplemented EasyDesign, ADAPT, and BADGERS algorithms in Rust with ONNX Runtime — 10–145× faster with identical results. All in a single place.

0×

Peak speedup

Cas12 vs EasyDesign

0%

Less peak memory

Cas12 vs EasyDesign

0×

Faster optimizer

Multi-target vs BADGERS

SPACER (Rust)Python

Cas12

Wall time56× faster
Peak memory78% less

Cas13

Wall time20.5× faster
Peak memory46% less

Multi-target

Wall time10.2× faster
Peak memory53% less

Variant-ID

Wall time9.8× faster
Peak memory79% less

Apple M4 Pro · 12 cores · 24 GB RAM · 10 iterations · median reported

Full methodology, reproduction scripts, and raw timing data available in the documentation.