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data
plots
scripts
.gitignore
README.md
call_variants.sh
call_variants_pileup.sh
simulate_reads.sh
trim_bam.sh

README.md

Validation of iVar

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.

Details:

Command Validated Against
trim cutadapt, Trimmomatic
consensus Geneious
variants VarScan2