CryptoNet: Cryptosporidium Whole Genome Sequence Nextflow Pipeline - CryptoSSU

Version: 1.0.0

Organization: NCEZID - Division of Foodborne, Waterborne, and Environmental Diseases (DFWED)

Contact Email: ncezid_shareit@cdc.gov

Description: CryptoSSU is a Nextflow DSL2 pipeline designed for molecular detection and species/subtype identification of Cryptosporidium from whole genome (isolate) or metagenomic sequencing. Built for the CDC’s CryptoNet program, the pipeline leverages containerization (Docker/Singularity) to ensure easy deployment, reproducibility, and modular maintenance across Unix-based computing environments.

Exemption: Non-exempt

Keywords: pathogen surveillance, next generation sequencing, bioinformatics, genomics, metagenomics, parasitic disease, Cryptosporidiosis

⚠️ Note: The results produced by this pipeline are not ISO or CLIA-certified and should not be considered diagnostic.

Overview

CryptoSSU is a Nextflow DSL2 pipeline designed for molecular detection and species/subtype identification of Cryptosporidium from whole genome (isolate) or metagenomic sequencing. Built for the CDC’s CryptoNet program, the pipeline leverages containerization (Docker/Singularity) to ensure easy deployment, reproducibility, and modular maintenance across Unix-based computing environments.

Pipeline Features

The pipeline identifies Cryptosporidium species using a BLAST-based 18S approach and gp60 subtyping. Key processing steps include:

1. Read Quality Control
   Tool: FastQC

2. Adapter Trimming
   Tool: fastp

3. Host/Prokaryotic Read Removal (optional)
   Tool: Kraken 2

4. De novo Assembly
   Tools (choice of one):

   • Unicycler
     
   • SKESA

5. Species Detection

Tool: Blast based approach using 18S sequence

1. GP60 Subtype Characterization

Tool: Blast based approach using GP60 subtype sequences

1. MultiQC Report

Tool: HTML or text document that summarizes the pipeline results into a report document

Usage

To run the pipeline:

```bash nextflow run CDCgov/WDPBCryptoSSU -r main \ -profile singularity \ -c \ --outdir

\ --platform illumina \ --allele

seq assets/allalleles_0.fasta \ --input

```

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