virology-bioinformatics
Viral genome assembly, intra-host variant calling, phylodynamics, and real-time surveillance.
Quick Reference
| Task | Tool | Notes | |------|------|-------| | Trim ARTIC primers | iVar trim | -b primer.bed -e | | Align to reference | Minimap2 / BWA-MEM | -ax sr for Illumina | | Consensus genome | iVar consensus | -t 0.5 (majority base) | | Low-freq variants | LoFreq | SNV at ≥ 1% frequency | | Clade assignment | Nextclade | SARS-CoV-2, flu, RSV | | Lineage
[Description truncada. Veja o README completo no GitHub.]