mod_bio

mod_bio implements Apache HTTP server modules to enable access and querying of genomic data formats (fastq, tabix, fasta, bam), leveraging the htslib C library for high-throughput sequencing data handling and supporting JSON-P for cross-domain data exchange.

Key Features:

• Apache HTTP modules: Implemented as modules for the Apache HTTP server to serve and query genomic files over HTTP.
• htslib integration: Integrates the htslib C library for handling high-throughput sequencing data and file operations.
• Supported file formats: Directly accesses and queries fastq, tabix, fasta, and bam file formats.
• Output formats: Returns data in plain text, HTML, XML, JSON, and JSON-P formats.
• Web querying: Exposes querying functionality for genomic files via HTTP requests.
• Cross-domain services: Provides JSON-P–based communication to enable cross-domain data retrieval.
• JavaScript genome browser: Includes a JavaScript-based genome browser component that uses JSON-P for data communication.

Scientific Applications:

• Sequence analysis: Delivers and queries sequencing data to support sequence analysis workflows.
• Variant calling: Facilitates access to BAM and tabix files for variant calling pipelines.
• Genome browsing and visualization: Serves genomic regions and annotations to genome browsers for visualization.

Methodology:

Implemented as Apache HTTP server modules, integrating the htslib C library for handling high-throughput sequencing formats and using JSON-P for cross-domain communication with a JavaScript-based genome browser.