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is a command-line and GUI-assisted pipeline for detecting, annotating, and visualizing viral vector integration sites from next-generation sequencing data (e.g., LAM-PCR, sonication-linked LM-PCR). It processes FASTQ files, maps reads to a reference genome and viral vector sequence, extracts integration junctions, and provides statistical summaries.

Main integration site detection.

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viatoolbox report -i all_annotated.tsv -o final_report/ is a command-line and GUI-assisted pipeline for detecting,

It is particularly valuable for: