ViralQC
  • Installation
    • Prerequisites
    • Installation via pip
      • Step 1: Install Dependencies
      • Step 2: Install ViralQC
      • Step 3: Verify Installation
    • Installation from Source Code
      • Step 1: Clone the Repository
      • Step 2: Create Conda Environment
      • Step 3: Install ViralQC
      • Step 4: Verify Installation
    • Docker
      • Step 1: Clone the Repository
      • Step 2: Build the Docker Image
      • Step 3: Verify Installation
      • Step 4: Run viralQC
  • Dataset Configuration
    • datasets.yml File Structure
    • Nextclade Datasets
    • GitHub Datasets
    • Configuration Parameters
  • Scoring Logic
    • Why a Custom System?
    • Quality Metrics
      • 1. missingDataQuality - Missing Data Quality
      • 2. privateMutationsQuality - Private Mutations Quality
      • 3. mixedSitesQuality - Mixed Sites Quality
      • 4. snpClustersQuality - SNP Clusters Quality
      • 5. frameShiftsQuality - Frameshifts Quality
      • 6. stopCodonsQuality - Stop Codons Quality
    • genomeQuality Calculation
    • Target Region Extraction
  • Commands and Usage
    • get-nextclade-datasets
      • Usage
      • Parameters
      • Output Structure
    • get-blast-database
      • Usage
      • Parameters
      • Release Date Filtering
      • Database Version
      • Output Structure
    • run
      • Usage
      • Required Parameters
      • Output Parameters
      • Dataset Parameters
      • Nextclade Sort Parameters
      • BLAST Parameters
      • BLAST Task Types
      • System Parameters
      • Complete Example
      • Analysis Workflow
    • API
      • Usage
      • Attributes and Methods
  • Preparing NCBI Submissions
    • Grouping by Virus (virus)
      • Supported Viruses
        • SARS-CoV-2
        • Dengue
        • Influenza
        • Norovirus
        • Custom Viruses
    • Grouping by Sample (sample)
    • Metadata CSV
      • Input Columns
        • Required Columns
        • Optional Columns — Standard Viruses (Dengue, Influenza, Norovirus, SARS-CoV-2)
        • Optional Columns — Custom Viruses
      • Output Format
    • FASTA Headers and Annotations
    • Batch Splitting
    • Python API
      • Installation
      • Constructor
      • Methods
        • run_virus(virus="all", virus_name=None)
        • run_sample(samples=["all"])
      • Return Value
      • Examples
        • Process all viruses found in the results file
        • Process only specific sample IDs
        • Process a custom virus with segment splitting
  • How to Add New Datasets
    • Adding a Nextclade Dataset
      • Step 1: Identify the Dataset
      • Step 2: Edit datasets.yml
      • Step 3: Obtain Taxonomic Information
      • Step 4: Test
    • Adding a GitHub Dataset
      • Step 1: Prepare Repository
      • Step 2: Add to datasets.yml
      • Step 3: Test
  • Output Structure
    • Main File: results.tsv (or .csv, .json)
      • 1. Sequence Identification
      • 2. Quality Metrics (ViralQC A-D System)
      • 3. Quality Metrics (Nextclade)
      • 4. Coverage and Regions
      • 5. Nucleotide Mutations
      • 6. Amino Acid Mutations
      • 7. Private Mutations (Detailed)
    • Target Regions Files
      • sequences_target_regions.bed
      • sequences_target_regions.fasta
    • Annotation Files
      • gff_files/
        • gff_files/per_sample/
      • tbl_files/
        • tbl_files/per_sample/
  • Practical Examples
    • Example 1: Basic Dengue Analysis
    • Example 2: Influenza (Multiple Segments)
    • Example 3: Metagenomic Analysis
    • Example 4: Reproducible Database
    • Example 5: JSON Output
    • Example 6: Sensitive BLAST Search
  • Troubleshooting
    • Problem 1: vqc command not found
    • Problem 2: Error downloading datasets
    • Problem 3: BLAST database not found
    • Problem 4: No sequences mapped
    • Problem 5: Memory errors
    • Problem 6: Permission denied
    • Problem 7: GitHub datasets not downloaded
    • Getting Help
  • Developer Guide
    • Dataset Management
      • get_github_dataset.py
      • jsonl_to_gff.py
      • get_minimizer_index.py
    • Analysis Pipeline
      • format_nextclade_sort.py
      • blast_wrapper.py
      • reorder_cds.py
      • post_process_nextclade.py
      • extract_target_regions.py
ViralQC
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