SAM - Sequence Assembly Manager

SAM - Sequence Assembly Manager manages whole genome shotgun sequence and whole genome assembly data to support storage, analysis, CGI-based visualization, and comparison of assemblies, including validation against fingerprint maps.

Key Features:

• Data Management: A MySQL relational database stores and organizes whole genome shotgun sequences and whole genome assembly data.
• Analysis Coordination: Perl applications perform processing and analysis of sequence and assembly datasets.
• Visualization and Reporting: CGI-based visualization and reporting components present assembly status and metrics for monitoring progress.
• Comparative Analysis: Functionality to compare sequence assemblies with fingerprint maps, applied to genomes such as Rhodococcus sp.RHAI and Cryptococcus neoformans WM276.

Scientific Applications:

• Genome Assembly Validation: Comparison of sequence assemblies to fingerprint maps to validate and refine genome assemblies.
• Progress Monitoring: Visualization outputs enable monitoring of assembly progress and status during whole genome sequencing projects.
• Data Integration and Analysis: Integration of diverse genomic datasets via MySQL and analysis using Perl applications to support downstream interpretation.

Methodology:

Uses a MySQL relational database for data storage, Perl applications for sequence and assembly processing, CGI-based components for visualization, and comparison of assemblies with fingerprint maps.