Cortex

Cortex implements colored de Bruijn graph algorithms to perform de novo assembly and to detect and genotype simple and complex genetic variants, including structural variants and HLA-B alleles, without requiring consensus reference assemblies.

Key Features:

• De Novo Assembly Using Colored De Bruijn Graphs: Assembles sequences directly using colored de Bruijn graphs to represent multiple samples and sequence variation.
• Variant Detection (High-Coverage): Detects and genotypes simple and complex structural variants in individual high-coverage genomes.
• Variant Detection (Low-Coverage/Pooled Data): Identifies sequences absent from the reference and calls variants from pooled low-coverage data, as applied to the 1000 Genomes Project.
• Reference-Free Variant Calling: Calls variants without a reference by leveraging population-level information, demonstrated in analyses of chimpanzee samples.
• HLA Genotyping: Estimates classical HLA genotypes, including HLA-B, from sequence assembly and variant calls.
• Low-Memory, Multi-Sample Assembly: Provides efficient, low-memory algorithms that support simultaneous assembly of multiple eukaryotic genomes.

Scientific Applications:

• De Novo Assembly: Reconstruction of genomic sequences from sequencing reads without reliance on a reference genome.
• Structural Variant Discovery and Validation: Detection and validation of structural variations within high-coverage human genomes.
• Novel Sequence Discovery: Identification of sequences absent from the reference genome using pooled low-coverage data.
• Population Reference-Free Genomics: Population-level variant calling without a reference, exemplified by chimpanzee studies.
• HLA Genotyping and Immunogenetics: Genotyping of highly polymorphic loci such as HLA-B for immunogenetic analyses.

Methodology:

Uses de Bruijn graph-based algorithms—specifically colored de Bruijn graphs—to assemble sequences and call variants, supports simultaneous assembly of multiple genomes, and leverages population information and pooled low-coverage data for reference-free variant calling.