VAAL

VAAL detects genetic variants from massively parallel DNA sequencing data to identify single nucleotide polymorphisms, insertions, deletions and more complex variants across bacterial genomes for comparative microbial genomics and antibiotic resistance research.

Key Features:

• Variant types detected: Identifies single nucleotide polymorphisms (SNPs), insertions, deletions (indels) and more complex or large insertion-deletion events across bacterial genomes.
• Input data: Operates on massively parallel DNA sequence data.
• Comparative analysis: Detects genomic differences by comparing sequence data between bacterial strains.
• High sensitivity and specificity: Demonstrated identification of approximately 98% of genomic differences between pairs of strains from three bacterial species.
• False positive elimination: Reported to call no false positives, ensuring identified variants represent genuine differences between compared genomes.
• Empirical validation: Successfully pinpointed the single mutation in Vibrio cholerae that conferred drug resistance by comparing drug-sensitive and drug-resistant strains.

Scientific Applications:

• Microbial Genomics: Accurate identification of genomic differences supports studies of bacterial evolution, diversity and strain comparison.
• Antibiotic Resistance Research: Pinpoints mutations associated with drug resistance, exemplified by detection of the resistance-causing mutation in Vibrio cholerae.

Methodology:

Processes massively parallel DNA sequence data and compares sequences between bacterial strains to detect SNPs, insertions, deletions and complex variants.