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bioRxiv · 10.1101/2020.01.26.914861

GS-Preprocess: Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility

Rodriguez, T. C.·Pratt, H. E.·Liu, P.·Amrani, N.·Zhu, L. J.
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Abstract

RNA-guided nucleases (e.g. CRISPR-Cas) are used in a breadth of clinical and basic scientific subfields for the investigation or modification of biological processes. While these modern platforms for site-specific DNA cleavage are highly accurate, some applications (e.g. gene editing therapeutics) cannot tolerate DNA breaks at off-target sites, even at low levels. Thus, it is critically important to determine the genome-wide targeting profile of candidate RNA-guided nucleases prior to use. GUIDE-seq is a high-quality, easy-to-execute molecular method that detects and quantifies off-target cleavage. However, this method may remain costly or inaccessible to some researchers due to its library sequencing and analysis protocols, which require a MiSeq platform that must be preprogramed for non-standard output. Here, we present GS-Preprocess, an open-source containerized software that can use standard raw data output (BCL file format) from any Illumina sequencer to create input for the Bioconductor GUIDEseq off-target profiling package. Single-command GS-Preprocess performs FASTQ demultiplexing, adapter trimming, alignment, and UMI reference construction, improving the ease and accessibility of the GUIDE-seq method for a wide range of researchers.

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Rodriguez, T. C., Pratt, H. E., Liu, P., Amrani, N., Zhu, L. J.. 2020-01-27. GS-Preprocess: Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility. https://doi.org/10.1101/2020.01.26.914861

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