CRISPRbuilder-TB

CRISPRbuilder-TB reconstructs complete CRISPR loci and associated Cas loci from Mycobacterium tuberculosis complex whole-genome sequencing (WGS) short reads to characterize spacer and direct repeat variation, duplications, and IS6110 insertions for evolutionary and diversity analyses.

Key Features:

• Accurate reconstruction: Reconstructs full CRISPR loci from simulated and real short read sequences (SRAs) to recover locus architecture beyond presence/absence spoligotyping profiles.
• Spacer and direct repeat mutation detection: Identifies mutations and variants within spacers and direct repeats.
• Mobile element insertion identification: Detects insertion sites of mobile elements such as IS6110 within CRISPR loci.
• Duplication recognition: Recognizes duplications within the CRISPR locus that are often missed by traditional methods.
• Cas locus reconstruction: Reconstructs the Cas locus alongside CRISPR arrays for a comprehensive view of the CRISPR system.
• Semi-automatic contig-based pipeline: Produces contigs from WGS short reads that can be assembled into complete CRISPR loci, with contig count influenced by SRA quality and read length.
• Robustness and precision: Provides more precise and robust reconstructions than generalist tools and can reveal erroneous CRISPR annotations in public MTC genomes.

Scientific Applications:

• CRISPR diversity and evolution in MTC: Enables in-depth analysis of CRISPR locus diversity, evolutionary mechanisms, and functional adaptations in Mycobacterium tuberculosis complex.
• Detection of adaptive events: Captures duplications, spacer variants, direct repeat mutations, and IS6110 insertions to study adaptive strategies and locus evolution.
• Cross-species CRISPR studies: Facilitates application of locus reconstruction approaches to other bacterial species that harbor similar CRISPR-Cas systems.

Methodology:

Semi-automatic pipeline that produces contigs from WGS short reads (SRAs) and reconstructs CRISPR arrays and Cas loci while detecting spacer and direct repeat mutations, IS6110 insertion sites, and duplications.