genome-editing

List of software/websites/databases/other stuff for genome engineering

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

FlashFry: The rapid CRISPR target site characterization tool

Automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif

Variant- and Haplotype-aware CRISPR guide design toolkit

BEstimate, a Python module that systematically analyses guide RNA (gRNA) targetable sites across given sequences for given Base Editors, and functional and clinical effects of the potential edits on the resulting proteins.

IES retention analysis from PacBio CCS reads

Comparing Cas Activities by Target Superimposition (CATS)

ALLEGRO is a synthetic biology tool that designs minimal, high activity CRISPR-Cas sgRNA libraries

A large scale off-target analysis tool for CRISPR/Cas9 genome editing system

Meganucleases|ZFNs|TALENs|CRISPR-Cas|BaseEditors|PrimeEditor

A kinetic model of CRISPR-Cas target recognition.

Transcript-unit architecture database for disease-associated large-fragment genome-writing target review.

Configurable literature collection, triage, ranking, and AI-summarization engine behind Papertrail.

This project critically analyzes the data pipeline of EVO 2, a cutting-edge AI model for genomic research developed by the Arc Institute and collaborators. The focus lies in evaluating its risks, ethical challenges, and governance structures in the context of data privacy, genome editing, and AI-driven biomedical innovation.

A desktop workstation for non-destructive genome variant editing, prediction and comparison, inspired by digital audio workstations.

Annotates CRISPR–Cas repair outcomes from CRISPResso2 allele tables: cut geometry (blunt vs staggered), deletion orientation and size, microhomology context, and which DNA end participates in repair — with publication-ready charts and statistics.

A declarative DSL and compiler for reproducible gene-editing design — with LLM agents and an MCP server so any AI agent can drive it safely.

Source-aware benchmark and validation-priority resource for high-mismatch genome-editing off-target prioritization.

A variant-first, multi-modality CRISPR design framework that unifies SpCas9 nuclease, base-editor, and prime-editor chemistries under a single typed interface to deliver ranked candidate edits complete with calibrated uncertainty intervals, predicted outcome distributions, and ancestry-stratified, population-aware off-target safety reporting.