Viral genome assembly, intra-host variant calling, phylodynamics, and real-time surveillance.
/plugin marketplace add Pavel-Kravchenko/Bioinformatics
The exact command may vary by repository. Check the README on GitHub.
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Viral genome assembly, intra-host variant calling, phylodynamics, and real-time surveillance.
| 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.]
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