Samscope

Samscope visualizes SAM/BAM alignments and NGS-derived features such as coverage, allele frequency, and polarity across whole-genome datasets to support ChIP-Seq and RNA-Seq analyses.

Key Features:

• Large dataset handling: Visualizes whole-genome datasets up to 3 Gb, including the entire human genome.
• Complex feature visualization: Displays coverage, allele frequency, and polarity across multiple experiments.
• Paging-friendly binary layout: Employs a paging-friendly binary file layout to enable processing of datasets larger than system RAM.
• OpenGL acceleration: Uses OpenGL for accelerated rendering and fast multi-resolution access to data.
• Cross-experiment analysis: Supports simultaneous or sequential viewing of features from multiple SAM/BAM files for comparative analysis.

Scientific Applications:

• Genomics: Inspection of whole-genome alignments and genomic variations using SAM/BAM data.
• Transcriptomics: Visualization and exploration of RNA-Seq alignments and gene expression patterns.
• Epigenetics: Visualization of ChIP-Seq data and chromatin modification profiles.

Methodology:

Implemented in C++ for Linux, Samscope uses OpenGL for rendering, a paging-friendly binary file layout, and extensive pre-processing to optimize SAM/BAM data handling and visualization.