Parapipe

Parapipe automates high-throughput analysis of Cryptosporidium next-generation sequencing data for genomic surveillance and epidemiological investigation.

Key Features:

• Modular Architecture: Built using Nextflow DSL2 with Singularity containerization for portability and scalability.
• ISO-Accreditable Framework: Validated for use in public health laboratory settings.
• Mixed Infection Analysis: Facilitates detection and analysis of mixed Cryptosporidium infections.
• Phylogenomic Clustering: Integrates phylogenomic analysis with epidemiological metadata for transmission pathway investigation.
• Whole-Genome Phylogenetic Resolution: Generates substantially greater phylogenetic resolution than conventional gp60 molecular typing in Cryptosporidium parvum.
• Automated Genomic Characterization: Delivers detailed genomic characterization through streamlined, reproducible workflows.

Scientific Applications:

• Cryptosporidium Genomic Surveillance: Supports public health monitoring of Cryptosporidium epidemiology, transmission and diversity.
• Outbreak Source Identification: Investigates complex transmission pathways and identifies sources of cryptosporidiosis outbreaks.
• Comparative Genomics: Applicable to analysis of NGS data from Cryptosporidium and related taxa.
• Population Diversity Studies: Improves understanding of Cryptosporidium population structure through whole-genome analysis.

Methodology:

Parapipe is built using Nextflow DSL2 and containerized with Singularity. Validation was performed using both simulated and real Cryptosporidium datasets.