cDNA-detector

cDNA-detector identifies and eliminates exogenous cDNA contamination in next-generation sequencing (NGS) data to prevent artifactual read coverage and incorrect peak calls.

Key Features:

• Implementation: Implemented in Python for computational detection and removal of contaminants.
• Contamination target: Detects exogenous cDNA that appears as additional read coverage over genes in NGS libraries.
• Sequencing types supported: Applicable to ATAC-Seq, ChIP-Seq, and whole-exome sequencing (WES) data.
• Detection approach: Identifies anomalous read coverage patterns indicative of contaminant genes.
• Impact on analysis: Eliminates contaminant genes that contribute to inaccurate coverage peak calls.
• Validation datasets: Evaluated on public repositories including TCGA, ENCODE, and NCBI SRA.

Scientific Applications:

• NGS quality control: Screening sequencing libraries for exogenous cDNA contamination to improve data integrity.
• Peak-calling accuracy: Preventing artifactual peaks in ATAC-Seq and ChIP-Seq analyses caused by contaminant coverage.
• Coverage refinement in WES: Improving accuracy of gene coverage estimates in whole-exome sequencing.
• Public dataset curation: Identifying contaminant genes in TCGA, ENCODE, and NCBI SRA datasets to refine sequence processing pipelines.

Methodology:

Detects anomalous read coverage patterns—additional read coverage over genes in NGS libraries—to identify and eliminate exogenous cDNA contaminant genes.