XenoCP

XenoCP removes mouse-derived reads from xenograft next-generation sequencing (NGS) BAM files to produce human-only BAMs for accurate downstream genomic analyses.

Key Features:

• BAM-to-BAM decontamination: Processes BAM files to remove mouse-specific sequences and outputs cleaned human BAM files.
• Mouse-read identification: Identifies sequences characteristic of the mouse genome to distinguish and filter contaminating reads from human reads.
• Cloud-based implementation: Runs on cloud platforms to provide scalable processing of xenograft sequencing datasets.

Scientific Applications:

• Xenograft sequencing for brain and solid tumor models: Removes mouse contamination from NGS data derived from human tumor xenografts in immunocompromised mice, including brain and solid tumors.
• RNA-seq gene expression quantification: Improves accuracy of gene expression estimates by eliminating mouse reads that confound RNA-seq analyses.
• Whole-genome sequencing (WGS) tumor heterogeneity assessment: Enables more accurate assessment of tumor heterogeneity in WGS by removing mouse-derived sequence artifacts.

Methodology:

Identifies and removes sequences characteristic of the mouse genome from input BAM files to isolate human genetic material; implemented to run on cloud platforms for scalable processing.