mapperanalyzer

MapperAnalyzer processes alignment output files from various aligners to extract detailed alignment statistics and convert results into BED and GBrowse formats for downstream genomic analysis and visualization.

Key Features:

• Output Analysis: Reads output files from alignment tools and extracts detailed statistical data about sequence alignments.
• Format Translation: Converts alignment outputs into BED and GBrowse formats for genome browsers and downstream pipelines.
• Parsing and Interpretation: Parses alignment data to derive alignment quality metrics and alignment characteristics.
• Galaxy Integration: Can be executed within Galaxy environments and integrated into Galaxy workflows, including deployments such as Galaxy@Pasteur.
• API and Automation: Integrates with execution engines via APIs or libraries such as Bioblend for automated workflow execution.

Scientific Applications:

• Alignment Quality Assessment: Provides statistics to evaluate the quality and characteristics of sequence alignments generated by different aligners.
• Genome Browser Visualization: Enables visualization of alignment results in genome browsers by converting outputs to BED or GBrowse formats.
• Reproducible Computational Workflows: Supports reproducibility and validation of computational biomedical research by producing standardized outputs and integrating into workflow systems.

Methodology:

Parses alignment output files to extract statistical metrics, converts outputs to BED and GBrowse formats, and can be invoked within Galaxy workflows or via APIs such as Bioblend (including Galaxy@Pasteur deployments).