This repository consists of a snakemake workflow dedicated to the analysis of libraries derived from the GUIDE-Seq protocol, including iGUIDE-Seq, GUIDE-Seq2, Tag-Seq, OliTag-Seq or any other libraries based on the original protocol by Tsai et al. 2015.
The key features of the pipeline are :
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High versatility with analysis of multiplexed libraries including samples from different organisms, gRNA and PAM sequences, PCR orientations ... in a single run.
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Quantification based on UMI or fragment length.
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Possibility to analyze already demultiplexed libraries with UMI extraction from read header if necessary.
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Possibility to merge samples at demultiplexing step (replicates, PCR orientation ...).
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Consideration of bulges and mismatches between the gRNA and gDNA alignments.
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Consideration of multi-hit reads (assignment to random position among best hits).
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Prediction of Off-target sites using SWOFFinder.
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Annotation to gene and oncogene (user defined lists).
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Reporting with QC and OT quantification.
This work is distributed under an Academic Non-Commercial License. Commercial use is not permitted without explicit written consent from the authors. See the LICENSE file for details.
If you use this pipeline in your research, please cite:
Repository : https://github.com/gcorre/GENETHOFF
DOI: 10.5281/zenodo.16759028
Publication : bioRxiv https://doi.org/10.1101/2025.09.30.679427
For installation and usage instructions, please read the complete documentation.