MagicViewer

MagicViewer visualizes short-read mappings from next-generation sequencing platforms (Roche 454, ABI SOLiD, Illumina) and annotates genetic variations against a reference genome to support variant detection and interpretation.

Key Features:

• Short-read mapping visualization: Visualizes mapped short reads against a reference genome for large-scale next-generation sequencing data.
• Genetic variation detection and filtering: Detects and filters genetic variations identified from mapped reads.
• Variation annotation and functional classification: Annotates genetic variations and provides functional classification of variants.
• Search and subset selection: Provides detailed search options and subset selection for focused analysis of variants.
• Sequence association and primer design: Associates sequence contexts with variants and offers primer design functionality.
• Platform support: Supports data generated by Roche 454, ABI SOLiD, and Illumina sequencing technologies.

Scientific Applications:

• Genome re-sequencing: Detection and annotation of variants in genome re-sequencing projects.
• Transcriptome studies: Analysis of short-read mappings and variant annotation in transcriptome sequencing.
• Variant interpretation: Functional classification and sequence association to aid interpretation of genetic variations.
• Targeted assay design: Primer design for downstream validation or targeted sequencing assays.

Methodology:

Computational pipeline performs short-read mapping to a reference genome followed by detection, filtering, annotation, visualization of genetic variations, and supports search, functional classification, subset selection, sequence association, and primer design.