GS-Preprocess

GS-Preprocess prepares input data for the Bioconductor GUIDEseq package by automating FASTQ demultiplexing, adapter trimming, read alignment, and UMI reference construction to enable genome-wide off-target profiling of RNA-guided nucleases such as CRISPR-Cas.

Key Features:

• Containerized distribution: Packaged as an open-source container to provide reproducible execution environments.
• Illumina BCL compatibility: Processes standard raw BCL output from Illumina sequencers.
• GUIDEseq input generation: Produces the required GUIDEseq inputs, including a 2-line guideRNA FASTA, demultiplexed "plus" and "minus" strand BAM files, and UMI references for each read.
• Single-command pipeline: Runs as a one-line pipeline that accepts six arguments to generate GUIDEseq input files.
• Automated data processing: Implements FASTQ demultiplexing, adapter trimming, alignment to a reference genome, and UMI reference construction.

Scientific Applications:

• GUIDE-seq data preparation: Prepares formatted inputs for Bioconductor GUIDEseq analyses of OFF-target events.
• Genome-wide off-target profiling: Enables identification and quantification of off-target cleavage events for RNA-guided nucleases including CRISPR-Cas systems.
• Nuclease specificity validation: Supports assessment of nuclease specificity to inform safety and efficacy evaluations in gene-editing therapeutics.

Methodology:

Performs FASTQ demultiplexing, adapter trimming, alignment to a reference genome, UMI reference construction, and outputs demultiplexed plus/minus-strand BAM files and GUIDEseq input files from Illumina BCL or FASTQ inputs.