MIRUReader

MIRUReader performs in-silico MIRU-VNTR typing of the Mycobacterium tuberculosis complex (MTBC) using long-read sequencing data (Pacific Biosciences and Oxford Nanopore Technologies) to derive 24-locus VNTR patterns for epidemiological genotyping.

Key Features:

• 24-locus MIRU-VNTR typing: Analyzes the 24 MIRU-VNTR loci specific to MTBC to determine locus-specific VNTR patterns.
• Long-read compatibility: Directly analyzes long sequence reads from Pacific Biosciences and Oxford Nanopore Technologies to cover entire repeat regions within each locus.
• Raw reads and assemblies: Processes both raw long reads and assembled genomes as input.
• VNTR identification and analysis: Identifies and analyzes variable number tandem repeats (VNTRs) across MIRU loci for pattern determination.
• Short-read limitation mitigation: Overcomes limitations of short-read sequencing (Illumina) by enabling repeat-region-spanning analyses.
• Epidemiological genotyping output: Produces detailed MIRU-VNTR patterns for strain differentiation and transmission inference.

Scientific Applications:

• Tuberculosis transmission tracking: Supports epidemiological studies that track MTBC transmission through VNTR-based genotyping.
• Strain differentiation and surveillance: Enables differentiation of MTBC strains using 24-locus MIRU-VNTR patterns for surveillance and outbreak investigations.
• Long-read VNTR analysis: Applied to long-read sequencing datasets (Pacific Biosciences, Oxford Nanopore Technologies) for comprehensive VNTR characterization.

Methodology:

Processes raw long reads and assembled genomes to identify and analyze variable number tandem repeats (VNTRs) across the 24 MIRU-VNTR loci of MTBC.