APHL-Infectious-Disease/group1

APHL-Infectious-Disease/group1

This repository contains a prototype pipeline developed for the 2026 APHL Hackathon by Group 1. All code, data products, and visualizations are for demonstration and development purposes only and should not be used for production, clinical, regulatory, or public health decision-making at this time.

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Introduction

APHL-Infectious-Disease/group1 is a Nextflow-based bioinformatics pipeline developed for the 2026 APHL Hackathon.

The pipeline enables re-analysis of publicly available sequencing data—particularly wastewater metagenomic datasets—to detect measles and enteric viruses of public health interest, including:

• Norovirus
• Rotavirus
• Enterovirus
• Astrovirus
• Adenovirus
• Sapovirus
• Poliovirus
• Morbillivirus

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Key Features

Multiple Input Modes

Mode	Description
--mode sra	Automatically discover datasets from NCBI SRA
--mode accessions	Use a user-provided list of SRR/ERR accessions
--mode samplesheet	Provide local FASTQ files

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Metadata Enrichment

• Pulls RunInfo metadata from SRA
• Enriches with BioSample metadata via NCBI E-utilities
• Extracts:
  • collection date
  • geographic location
  • isolation source
  • lat/lon (when available)
• Filters to U.S.-based samples

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Data Processing

• Parallel FASTQ download via fastq-dl
• Optional preprocessing (QC + trimming)
• Kraken2 classification against viral database

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Post-classification Analysis

Generates:

• metadata_postkraken.csv
• metadata_postkraken_hits_only.csv

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Optional Steps

Feature	Parameter
Preprocessing	--run_preprocessing
MultiQC report	--run_multiqc

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Workflow Overview

SRA / Accessions / Samplesheet
              ↓
         FASTQ Download
              ↓
        (Optional QC)
              ↓
           Kraken2
              ↓
     Metadata Enrichment
              ↓
    PostKraken Matrix Build
              ↓
       Results Dashboard

Subworkflows and Modules

SRA_DISCOVERY

• Uses Entrez to search SRA
• Retrieves RunInfo metadata
• Outputs accession list + metadata

FETCH_READS (FASTQDL)

• Downloads FASTQ files from SRA
• Supports parallel retrieval

MAKE_ACCESSIONS_METADATA

• Builds metadata for user-provided accessions
• Pulls SRA + BioSample metadata

ENRICH_SRA_METADATA

• Enhances SRA metadata with BioSample fields
• Improves completeness (dates, locations, etc.)

PREPROCESS_READS (Optional)

• Tools: fastp, FastQC, seqkit
• Performs trimming + QC

PREPARE_KRAKEN_DB

• Accepts:
  • local DB (--kraken2_db)
  • remote DB (--kraken2_db_url)
• Downloads and prepares database if needed

CLASSIFY_READS (Kraken2)

• Runs Kraken2 classification
• Produces per-sample reports

BUILD_POSTKRAKEN_MATRIX

• Combines:
  • Kraken reports
  • enriched metadata
• Generates final matrices

POSTKRAKEN_MATRIX

• Parses Kraken outputs
• Produces:
  • full matrix
  • hits-only matrix

QC REPORT (Optional)

• Generates MultiQC report

RESULTS DASHBOARD

bash shiny.sh

• shiny.sh launches app.R, which combines and saves kraken files as a single summary file and generates an associated dashboard from the kraken summary file and SRA metadata file
• This should automatically open the associated dashboard html. If not, got to Ports, select 8080 and click "open in browser" (the globe icon)

In a new codespace, it may be necessary to first run the following commands in the terminal:

conda install -c conda-forge r-base
conda install -c conda-forge r-tidyverse r-shiny r-leaflet r-thematic r-DT

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Usage

SRA Mode

nextflow run main.nf \
  -profile conda \
  --mode sra \
  --kraken2_db assets/kraken2db_v2 \
  --max_runs 20 \
  --outdir results

Accessions Mode

nextflow run main.nf \
  -profile conda \
  --mode accessions \
  --accessions docs/accessions.txt \
  --kraken2_db assets/kraken2db_v2 \
  --outdir results

Samplesheet Mode

nextflow run main.nf \
  -profile conda \
  --mode samplesheet \
  --input path/to/samplesheet.csv \
  --kraken2_db assets/kraken2db_v2 \
  --outdir results

Using a Remote Kraken2 Database

nextflow run main.nf \
  -profile conda \
  --mode samplesheet \
  --input path/to/samplesheet.csv \
  --kraken2_db_url https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20221209.tar.gz \
  --outdir results

Optional Parameters

Parameter	Description
--run_preprocessing	Enable QC + trimming
--run_multiqc	Generate MultiQC report
--max_runs	Limit SRA runs
--subsample_size	Subsample reads

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Output

File	Description
metadata_postkraken.csv	Full detection matrix
metadata_postkraken_hits_only.csv	Filtered detections
multiqc_report.html	QC summary (optional)
pipeline_info/	Execution logs + versions

Known Limitations

• SRA metadata may be incomplete or inconsistent
• BioSample metadata availability varies
• Detection thresholds not yet standardized
• Prototype only — not production ready

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Future Directions

• Improve SRA query strategy
• Add detection confidence scoring
• Expand pathogen panel
• Integrate dashboards
• Optimize performance at scale

Credits

APHL-Infectious-Disease/group1 was written by Group 1.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.