BamView

BamView visualizes sequence reads from next-generation sequencing (NGS) platforms aligned to a reference genome to support inspection of base qualities, coverage, variants, structural variation, and expression analyses.

Key Features:

• Multi-Level Visualization: Displays base qualities at nucleotide resolution and coverage at genome- and chromosome-level scales.
• Configurable Views: Supports overlaying multiple read alignment files from different experiments for comparative analysis.
• Data Filtering and Interpretation: Provides filtering of aligned reads based on specified criteria to refine analyses.
• Integration with Artemis Genome Browser: Integrates read alignments with reference genome sequences and annotations in the Artemis genome browser.
• SNP Analysis and Structural Variations: Highlights single nucleotide polymorphism (SNP) density and candidate SNP sites and uses read-pair information to identify large insertions and deletions.
• Mapping and Expression Analysis: Calculates read counts and reads per kilobase per million mapped reads (RPKM) for selected genes.

Scientific Applications:

• Comparative Genomics: Comparison of multiple alignment datasets to support comparative genomic analyses.
• SNP Discovery: Detection and inspection of candidate SNP sites and SNP density across regions.
• Structural Variation Analysis: Identification of large insertions and deletions using read-pair information.
• Gene Expression Profiling: Quantification of gene expression using read counts and RPKM metrics for selected genes.

Methodology:

Uses algorithms for read alignment visualization, highlights SNP density and candidate SNPs, utilizes read-pair information to detect large insertions and deletions, and computes read counts and RPKM for genes.