iVar

iVar analyzes viral amplicon-based sequencing data to quantify intrahost viral genetic diversity and assess experimental and biological factors that affect variant measurement.

Key Features:

• Integration with PrimalSeq: Processes multiplexed amplicon data generated by the PrimalSeq approach and evaluates effects of virus concentration, sequencing coverage, primer mismatches, and replicates on diversity measurements.
• Experimental protocol for sequencing: Provides a protocol tailored for measuring viral diversity using Illumina sequencing and enables comparisons with Oxford Nanopore sequencing.
• Measured virus targets: Demonstrated measurement of genetic diversity for viruses including Zika and West Nile across different sample types.
• Influence analysis: Assesses how experimental conditions and biological systems contribute to the accumulation of genetic diversity within viral populations.

Scientific Applications:

• Epidemiological studies: Provides intrahost diversity data to support tracking of viral spread and evolution within hosts.
• Vaccine development: Informs vaccine design by identifying prevalent strains and potential escape mutations within hosts.
• Antiviral resistance research: Enables study of intrahost diversity dynamics that underlie the emergence of antiviral resistance.

Methodology:

Processes multiplexed amplicon sequencing data (PrimalSeq) from Illumina and Oxford Nanopore to quantify intrahost viral diversity while accounting for virus concentration, sequencing coverage, primer mismatches, and replicate effects, and enables cross-platform comparisons.