gencore

gencore generates consensus reads and performs deduplication and error suppression on next-generation sequencing (NGS) data to reduce sequencing noise and improve detection of ultra-low frequency mutations from deep sequencing datasets.

Key Features:

• Deduplication with UMI Support: Handles unique molecular identifiers (UMIs) to distinguish reads derived from different original DNA fragments during deduplication.
• Error Suppression via Consensus Reads: Clusters mapped sequencing reads and merges them into consensus reads within each cluster to remove random errors introduced during library construction and sequencing.
• Performance Efficiency: Reports faster runtime, lower memory usage, and reduced mapping mismatches compared with Picard, SAMtools, UMI-Reducer, and UMI-tools.
• Informative Reporting: Outputs statistical results in HTML (including figures that plot coverage and duplication) and JSON formats for downstream analysis.

Scientific Applications:

• Ultra-low Frequency Mutation Detection: Improves accuracy of detecting ultra-low frequency mutations in deep sequencing datasets by suppressing sequencing errors and removing duplicates.
• Clinical and Cancer Genomics: Applicable to clinical NGS workflows, personalized medicine, and cancer research where high-accuracy variant calling is required.

Methodology:

Clusters mapped reads and generates consensus reads within each cluster for deduplication and error suppression.