detectIS

detectIS identifies precise exogenous DNA integration sites in host genomes from paired-end DNA or RNA sequencing data to characterize recombinant and viral integrations.

Key Features:

• Integration site identification: Pinpoints precise genomic locations of exogenous DNA integration events.
• Input data: Operates on paired-end sequencing data derived from DNA or RNA, including RNA-seq.
• Recombinant context support: Targets integrations arising from viral transduction and plasmid transfection in engineered cell lines.
• Workflow management: Implements a Nextflow workflow to orchestrate computational tasks.
• Containerization: Encapsulates required software components within a Singularity image.
• Validation: Tested on simulated datasets and on real human RNA-seq data infected with Hepatitis B virus.
• Comparative performance: Reported to outperform state-of-the-art tools by providing more precise results while reducing computational demands and execution times.

Scientific Applications:

• Recombinant cell line characterization: Defining integration loci for characterization of recombinant cell lines used in biology, medicine, and biotechnology.
• Viral integration analysis: Mapping integrations of Hepatitis B virus in human RNA-seq samples.
• Transduction and transfection assessment: Assessing genomic integration outcomes following viral transduction and plasmid transfection in engineered cell lines.

Methodology:

Analyzes paired-end DNA or RNA sequencing data to detect integration sites using a Nextflow-managed workflow packaged in a Singularity image; validation was performed on simulated datasets and human RNA-seq infected with Hepatitis B virus.