Viral-Specific Tools

Relevant source files

The following files were used as context for generating this wiki page:

• src/app/services/(viral-tools)/sars-cov2-genome-analysis/page.tsx
• src/app/services/(viral-tools)/subspecies-classification/page.tsx
• src/lib/services/service-info.ts
• src/lib/forms/(viral-tools)/subspecies-classification/subspecies-classification-form-schema.ts
• src/lib/forms/(viral-tools)/sars-cov2-genome-analysis/tests/sars-cov2-genome-analysis-form-utils.test.ts
• src/components/navbars/navbar-links.ts

Introduction

The Viral-Specific Tools module within DXKB provides a suite of specialized computational services designed for the analysis, classification, and assembly of viral genomic data. These tools cater to specific research needs for high-priority pathogens, including SARS-CoV-2, Influenza, and various other viral species identified by the International Committee on Taxonomy of Viruses (ICTV).

The module encompasses several key services:

• SARS-CoV-2 Genome Analysis: A meta-service for assembly, annotation, and variation analysis.
• Subspecies Classification: Genotype and subtype assignment using phylogenetic placement.
• SARS-CoV-2 Wastewater Analysis: Lineage and variant detection in environmental samples.
• Influenza HA Subtype Conversion: Structural-based numbering scheme conversion.
• Viral Assembly: Genome construction using the IRMA assembler.

Sources: src/components/navbars/navbar-links.ts:108-132, src/lib/services/service-info.ts:1010-1014

SARS-CoV-2 Genome Analysis

This tool functions as a "meta-service" that integrates multiple analytical workflows. It accepts either raw read files or pre-assembled contigs. When reads are provided, the system automatically invokes an assembly service before proceeding to annotation and variation analysis.

Workflow Logic

The service supports multiple assembly strategies, primarily focused on CDC and ARTIC protocols.

Key Parameters

Parameter	Type	Description
recipe	Enum	Assembly strategy (e.g., One Codex, CDC-Illumina, CDC-Nanopore).
primers	Enum	Primer set selection (ARTIC, midnight, swift, etc.) for One Codex strategy.
taxonomy_id	String	Pre-populated as 2697049 for SARS-CoV-2.
input_type	Enum	Toggle between 'reads' and 'contigs'.

Sources: src/app/services/(viral-tools)/sars-cov2-genome-analysis/page.tsx:392-414, src/lib/services/service-info.ts:1025-1065

Subspecies Classification

The Subspecies Classification tool assigns genotypes or subtypes to query sequences. It utilizes the pplacer tool to perform phylogenetic placement of query sequences within a reference tree and reference alignment.

Architecture and Data Flow

The tool interprets pplacer results using Cladinator to determine the specific clade assignment based on ICTV-maintained standards.

Supported Virus Types

The service supports a wide range of families, including:

• Flaviviridae: HCV, Dengue, Zika, West Nile, Yellow Fever.
• Adenoviridae: Human mastadenoviruses A-F.
• Caliciviridae: Norovirus (VP1/VP2).
• Orthomyxoviridae: Influenza A H5, Swine H1/H3.
  Source: src/lib/forms/(viral-tools)/subspecies-classification/subspecies-classification-form-schema.ts:14-41

SARS-CoV-2 Wastewater Analysis

This specialized service detects and quantifies lineages and Variants of Concern (VOC) in wastewater samples. It uses Minimap2 for alignment against the Wuhan-Hu-1 reference genome and Freyja for variant analysis.

Processing Pipeline

1. Alignment: Reads are aligned using Minimap2.
2. Conversion: SAMtools converts alignments to sorted BAM files.
3. Trimming: iVAR trims primers and low-quality sequences.
4. Quality Control: FastQC assesses raw and aligned data.
5. Lineage Quantification: Freyja analyzes variants to identify lineages.

Sources: src/lib/services/service-info.ts:1102-1107, src/lib/services/service-info.ts:1143-1150

Viral Assembly (IRMA)

The Viral Assembly service utilizes the Iterative Refinement Meta-Assembler (IRMA) to construct viral genomes. Unlike general-purpose assemblers, IRMA is optimized for highly variable viral populations.

Configuration

Users must select a Reference Database tailored to the target virus:

• FLU: Influenza viruses.
• CoV: Coronaviruses.
• RSV: Respiratory Syncytial Virus.
• EBOLA: Ebola virus.

Sources: src/lib/services/service-info.ts:1157-1159, src/lib/services/service-info.ts:1193-1198

Summary

Viral-Specific Tools in DXKB provide targeted analytical pipelines for critical human and animal pathogens. By integrating domain-specific tools like pplacer, IRMA, and Freyja, the system enables researchers to move from raw sequence data to high-resolution classification and variant identification within a unified workspace environment.

Sources: src/lib/services/service-info.ts:1010-1014, src/lib/services/service-info.ts:1172-1178