Scoring Logic

ViralQC implements its own quality scoring system that is more flexible than Nextclade’s standard system.

Why a Custom System?

While Nextclade uses three categories (good, mediocre, bad) based on fixed scores, ViralQC offers four levels (A, B, C, D):

A - Sequences meeting all quality criteria
B - Sequences suitable for most analyses
C - Use with caution
D - Use not recommended

Quality Metrics

ViralQC calculates scores for 6 metrics:

1. missingDataQuality - Missing Data Quality

Based on genome coverage:

Coverage	Score
≥ 90%	A
≥ 75%	B
≥ 50%	C
< 50%	D

2. privateMutationsQuality - Private Mutations Quality

Based on the number of private mutations relative to a configurable threshold:

Private Mutations	Score
≤ threshold	A
≤ threshold × 1.05	B
≤ threshold × 1.10	C
> threshold × 1.10	D

Default threshold: 10 mutations (configurable per virus via private_mutation_total_threshold)

3. mixedSitesQuality - Mixed Sites Quality

Mixed Sites	Score
0	A
1	B
2	C
≥ 3	D

4. snpClustersQuality - SNP Clusters Quality

SNPs Clustered	Score
0	A
1	B
2	C
≥ 3	D

5. frameShiftsQuality - Frameshifts Quality

Frameshifts	Score
0	A
1	B
2	C
≥ 3	D

6. stopCodonsQuality - Stop Codons Quality

Stop Codons	Score
0	A
1	B
2	C
≥ 3	D

genomeQuality Calculation

The overall genome score combines all 6 metrics:

Conversion: A=4, B=3, C=2, D=1 points
Normalization: score = (total / 24) × 24
Classification:

Score	genomeQuality
= 24	A
≥ 18	B
≥ 12	C
< 12	D

Target Region Extraction

ViralQC extracts sequences based on quality hierarchy:

        graph TD
    A[Analyze Sequence] --> B{genomeQuality = A or B?}
    B -->|Yes| C[Extract COMPLETE GENOME]
    B -->|No| D{targetRegionsQuality = A or B?}
    D -->|Yes| E[Extract TARGET REGIONS]
    D -->|No| F{targetGeneQuality = A or B?}
    F -->|Yes| G[Extract TARGET GENE]
    F -->|No| H[DO NOT EXTRACT]