CasCollect

CasCollect performs targeted assembly and annotation of Cas genes and CRISPR arrays directly from unassembled raw Illumina sequencing reads to detect and characterize CRISPR/Cas systems in isolate and metagenomic data.

Key Features:

• Targeted assembly and annotation: Performs targeted assembly and annotation of Cas genes and CRISPR arrays, including isolated arrays, from unassembled raw Illumina sequencing reads.
• Enhanced efficiency: Achieves assembly throughput reported as almost two orders of magnitude faster than conventional methods while maintaining detection accuracy for Cas genes and CRISPR arrays.
• Versatility and customization: Supports targeted assembly of arbitrary specialty gene sets and can be reconfigured to incorporate custom Hidden Markov Models (HMMs) or reference nucleotide sequences.
• Metagenomic applicability: Operates on metagenomic data to facilitate discovery of novel Cas genes from complex microbial communities.

Scientific Applications:

• Bacteriophage therapy research: Identifies CRISPR/Cas systems that inform pathogen susceptibility to bacteriophage therapy.
• Gene-editing discovery: Facilitates identification of novel Cas genes with properties relevant to gene-editing applications, particularly from metagenomic datasets.
• Study of microbial adaptive immunity: Enables exploration of adaptive immune systems in bacteria and archaea that defend against bacteriophages, plasmids, and foreign nucleic acids.

Methodology:

Processes unassembled raw Illumina sequencing reads, performs targeted assembly and annotation of Cas genes and CRISPR arrays (including isolated arrays), and supports incorporation of user-supplied Hidden Markov Models (HMMs) or reference nucleotide sequences; the approach is optimized for accelerated assembly.