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

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

FlashFry: The rapid CRISPR target site characterization tool

Core code for the DeepHF prediction tool

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Flexible analysis of high-content CRISPR screening

Comprehensive design of CRISPR gRNAs for nucleases and base editors

A software tool for personalized and allele-specific CRISPR editing.

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

Modelling insertion efficiency for Prime Insertion Experiments

a guideRNA database generation tool

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

Analyze CRISPR and shRNA functional genetic screening data