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

Synthego ICE - Inference of CRISPR Editing software

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

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

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Flexible analysis of high-content CRISPR screening

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

Collection of R packages that work in harmony for CRISPR gRNA design

CRISPR, faster, better – The Crackling method for whole-genome target detection

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.

Tutorials for the crisprVerse

ProTiler method for the analysis and visualization of CRISPR screens with tiling-sgRNA design

A cross-platform Graphical Analysis Tool for high-throughput CRISPR-based genome editing evaluation

Visualization of CRISPR guide RNAs (gRNAs)

Useful human and mouse data for the crisprVerse ecosystem

CB2-Experiments is the repository of scripts and data of experiments were performed to benchmark the performance of CB2.