Repository contains scripts used to validation of trimming, consensus calling and variant calling using iVar.
.
├── data
│ ├── alignments - Contains alignments of consensus sequences called using iVar, Geneious
│ ├── ref - Reference sequences used
│ └── variants - Variant csv and tsv files called using VarScan and iVar.
├── plots - Plots generated by R scripts and used to create validation figures.
└── scripts - Contains R scripts used to create validation figures and validate results.
| Command | Validated Against |
|---|---|
| trim | cutadapt, Trimmomatic |
| consensus | Geneious |
| variants | VarScan2 |