SVJedi

SVJedi genotypes structural variations (SVs) from Pacific Biosciences and Oxford Nanopore long-read sequencing data to provide allele-level SV genotypes for genomic analyses.

Key Features:

• Long Read Compatibility: Designed for Pacific Biosciences and Oxford Nanopore long-read sequencing datasets to leverage long-read information for SV genotyping.
• Allele-Specific Reference Generation: Generates allele-specific reference sequences representing the two alleles of each structural variant.
• Alignment and Filtering Process: Aligns long reads to allele-specific references and applies analysis and filtering to retain informative alignments for allele identification.
• Genotyping Output: Accepts a variant VCF, a reference genome (fasta), and long reads (fasta/fastq) and outputs an enhanced VCF with additional genotyping columns.
• Allele Frequency Estimation: Estimates allele frequencies based on counts of informative alignments.

Scientific Applications:

• Human genome SV genotyping: Genotyping structural variants in human genome analyses for research and diagnostic contexts.
• Method validation on datasets: Applicable to both simulated and real human datasets for validation and benchmarking.
• Clinical diagnostics: Enables precise characterization of SVs relevant to clinical diagnostic workflows.
• Comparative analyses: Improves SV genotyping accuracy compared to short read–based approaches and direct SV discovery techniques.

Methodology:

Generates allele-specific reference sequences for each structural variant; aligns long reads to these references; analyzes and filters alignments to quantify the presence of SV alleles; and estimates allele frequencies from informative alignment counts.