Picky

Picky detects structural variants in cancer genomes from long-read sequencing data (Oxford Nanopore and PacBio) to characterize complex rearrangements and breakpoint-level features.

Key Features:

• Long-Read Sequencing Compatibility: Operates on Oxford Nanopore and PacBio long-read data to resolve complex SV architectures that short-read methods often miss.
• Superior Specificity and Sensitivity: Identifies a broad spectrum of structural variants with enhanced specificity and sensitivity relative to traditional short-read analyses.
• Repetitive DNA Analysis: Detects and characterizes repetitive DNA sequences as significant sources of structural variation.
• Nucleotide-Resolution Breakpoint Mapping: Maps genome-wide breakpoints at nucleotide resolution and detects micro-insertions associated with SVs.
• Genomic Context Insights: Quantifies breakpoint density and interchromosomal connectivity and reports enrichment of breakpoints in promoters and transcribed regions.
• Detection of Reciprocal Translocations: Uses phased SV analysis to identify over-representation of reciprocal translocations resulting from chromosomal double-crossovers.

Scientific Applications:

• Cancer genomics: Accurate detection and characterization of SVs to investigate mechanisms of tumorigenesis and to aid identification of potential therapeutic targets and biomarkers.
• Structural variation research in complex diseases: Comprehensive analysis of SV landscapes and breakpoint features to study genetic diversity and genomic mechanisms in other complex diseases.

Methodology:

Uses Oxford Nanopore and PacBio long-read sequencing data to detect a full spectrum of structural variants, perform nucleotide-resolution breakpoint mapping including micro-insertion identification, analyze repetitive DNA sequences, apply phased SV analysis to detect reciprocal translocations from double-crossovers, and assess genome-wide breakpoint density and interchromosomal connectivity with enrichment evaluation in promoters and transcribed regions.