Olivar

Olivar automates variant-aware primer design for multiplex tiled amplicon sequencing of pathogen genomes by converting each nucleotide into a numeric risk score that captures undesired sequence features.

Key Features:

• Automated risk scoring: Converts each nucleotide of the target genome into a numeric risk score capturing undesired sequence features to avoid during primer design.
• Variant-aware design: Incorporates variant information to generate tiled amplicons in situations of high mutation frequency and/or density.
• Multiplex tiled amplicon generation: Produces complete tiled amplicon schemes for pathogen genome sequencing without downstream manual optimization.
• Reduced mismatches and byproducts: Produces fewer mismatches overlapping with primers and fewer predicted PCR byproducts compared to PrimalScheme.
• Validation against established primer sets: Achieves similar read mapping rates (~90%) and better coverage compared to ARTIC v4.1 amplicons for SARS-CoV-2 sequencing.
• Wastewater sample compatibility: Achieves up to 3-fold higher mapping rates while retaining similar coverage on real wastewater samples compared to existing approaches.

Scientific Applications:

• Pathogen genome surveillance: Enables tiled amplicon sequencing for tracking the spread and evolution of pathogens such as SARS-CoV-2.
• High-mutation pathogen sequencing: Generates tiled amplicons for pathogens with high mutation frequency and/or density where manual design is slow and costly.
• Wastewater-based epidemiology: Supports sequencing of pathogens from complex environmental samples such as wastewater.
• Multiplex PCR assay development: Automates the generation of tiled amplicon schemes for multiplexed pathogen detection and characterization.

Methodology:

Olivar converts each nucleotide of the target genome into a numeric risk score capturing undesired sequence features that should be avoided in primer design.