ReadDepth

ReadDepth: Copy Number Alteration Detection from Sequencing Data

ReadDepth detects copy number alterations (CNAs) from genome-wide sequencing data by modeling coverage depth with an overdispersion-aware statistical framework and refining breakpoints using paired-end sequencing information.

Key Features:

• High Accuracy and Speed: Implements multi-core parallel processing to analyze large sequencing datasets efficiently without reducing precision.
• No Reference Sample Required: Applies a statistical model that accounts for overdispersed data, eliminating the need for matched reference samples.
• Resolution Enhancement: Incorporates breakpoint information from paired-end sequencing to improve positional accuracy, including in low-coverage experiments.
• Integration with Epigenomic Data: Infers copy number from whole-genome bisulfite sequencing reads, enabling joint analysis of epigenomic and copy number alterations.
• Coverage Versatility: Maintains robust performance across genomes sequenced at varying coverage levels.

Scientific Applications:

• Cancer Genomics: Detects copy number alterations in tumor samples to study tumorigenesis, genomic instability, and interactions between genetic and epigenetic changes.

Methodology:

Quantifies genome-wide sequencing coverage depth and applies a statistical model to account for overdispersion in read counts. Uses breakpoint information from paired-end reads to refine the genomic positions of detected copy number alterations.