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

IES retention analysis from PacBio CCS reads

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

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.

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

ALLEGRO: An Algorithm Leveraging Linear Programing to Enhance Guide RNA Optimization

Benchmarking BleTIES with Tetrahymena long read data

Benchmarking BleTIES with simulated long reads

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

Source code and files for structural network analysis of Cas9 RNP