Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium.

ABSTRACT: Cryptosporidium, a protozoan parasite of significant public health concern, is responsible for severe diarrhoeal disease, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of whole-genome next-generation sequencing (NGS) data is critical in improving our understanding of Cryptosporidium epidemiology, transmission and diversity. However, effective analysis of NGS data in a public health context necessitates the development of robust, validated computational tools. We present Parapipe, an ISO-accreditable bioinformatic pipeline for high-throughput analysis of NGS data from Cryptosporidium and related taxa. Built using Nextflow DSL2 and containerized with Singularity, Parapipe is modular, portable, scalable and designe

SUBMITTER: Morris AV 

PROVIDER: S-EPMC12451305 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature