AmpliDiff

AmpliDiff finds highly discriminatory genomic regions in viral genomes and designs primers for their amplification, providing a cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.

Key Features:

• Discriminatory region identification: Simultaneously finds highly discriminatory genomic regions in viral genomes of a single species.
• Primer design: Designs primers allowing for the amplification of identified discriminatory regions.
• Lineage abundance estimation: Enables accurate estimation of relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data, with errors comparable to using whole genome information.
• Robustness to incomplete data: Performs robustly against incomplete input data.
• Temporal primer stability: Primers bind to genomes sampled months after the primers were selected.

Scientific Applications:

• Viral metagenomics: Estimates lineage abundances in viral metagenomes without requiring whole genome sequencing.
• SARS-CoV-2 surveillance: Estimates relative abundances of SARS-CoV-2 lineages in wastewater sequencing data.

Methodology:

AmpliDiff uses a computational approach to simultaneously find highly discriminatory genomic regions in viral genomes of a single species and design primers for their amplification through PCR.