BamHash

BamHash verifies that read pairs in FASTQ files match those in BAM files using checksum-based comparison to confirm sequence data integrity after alignment.

Key Features:

• Checksum-based verification: Generates checksums for read pairs to detect discrepancies between raw FASTQ reads and aligned BAM records.
• Order-independent comparison: Matches read pairs irrespective of file ordering in FASTQ and BAM.
• Read-pair level matching: Operates at the level of read pairs to ensure each pair corresponds between formats.
• C++ implementation: Implemented in C++ to provide performant execution for computational workflows.

Scientific Applications:

• FASTQ–BAM integrity verification: Confirms that raw sequencing reads (FASTQ) and their aligned counterparts (BAM) are consistent.
• Enabling safe deletion of redundant raw data: Provides evidence to support removal of FASTQ files after verified alignment to reduce storage requirements.
• Quality control in large-scale resequencing projects: Detects data corruption or mismatches and supports storage management in large resequencing efforts.

Methodology:

Generates checksums for read pairs from FASTQ and BAM files and compares those checksums irrespective of read order; implemented in C++.