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

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

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

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

Comparing Cas Activities by Target Superimposition (CATS)

A kinetic model of CRISPR-Cas target recognition.

ALLEGRO is a synthetic biology tool that designs minimal, high activity Cas9 guide RNA libraries

Accelerate DNA gene editing projects with intuitive, AI-powered CRISPR gRNA design and analysis

Benchmarking BleTIES with Tetrahymena long read data

Benchmarking BleTIES with simulated long reads

ALLEGRO is a synthetic biology tool that designs minimal, high activity Cas9 guide RNA libraries

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.

Lightweight Flask application for invoking machine learning-based predictive modeling of CRISPR/Cas9 guide efficiency.