2-kupl

2-kupl detects genomic variants between two matched DNA sequencing (DNA-seq) samples using a mapping-free k-mer–based comparative analysis.

Key Features:

• Mapping-Free Variant Detection: Identifies genomic variants without aligning reads to a reference genome by directly comparing k-mer content between samples.
• K-mer–Based Comparative Analysis: Uses k-mer subsequences derived from DNA-seq reads to detect point mutations, insertions and deletions (indels), and structural variants.
• Variant Detection in Complex Regions: Detects variants in genomic regions difficult to analyze using alignment-based methods, including regions with large indels, aggregated mutations, or repetitive sequences.
• Reference-Independent Analysis: Enables comparative genomic analysis in datasets lacking suitable reference genomes or containing unmappable genomic regions.
• Disease Variant Discovery: Identifies candidate variants, including potential recurrent variants detected in prostate cancer whole exome sequencing datasets.

Scientific Applications:

• Cancer Genomics: Enables detection of somatic variants in complex or poorly mappable genomic regions in cancer sequencing datasets.
• Microbial Comparative Genomics: Supports comparison of genomic variation between bacterial strains when reference genomes are incomplete or unavailable.
• Reference-Free Genomic Analysis: Facilitates variant discovery and comparative genomics in organisms lacking well-characterized reference genomes.

Methodology:

The tool extracts k-mers from DNA sequencing reads and compares their frequency and distribution between two matched samples to identify discrepancies indicative of genomic variants.