PrimalScheme

PrimalScheme designs primer panels for multiplex PCR to enable low-cost viral genome sequencing.

Key Features:

• Greedy algorithm primer design: Finds primers for tiling amplicon generation across multiple reference genomes.
• Discrete primer clouds: Expands amplicon sequencing to diverse virus species through improved primer design.
• PrimalScheme Labs integration: Supports a scheme repository for finding and sharing primer schemes with established data standards.
• High-diversity scheme capability: Generates primer schemes for viruses with high genetic diversity such as pan-genotype Measles virus.
• High-sensitivity short amplicon design: Produces schemes with over 1000 primers for low-titre clinical samples such as Monkeypox virus.

Scientific Applications:

• Viral genome sequencing: Supports amplicon sequencing of viruses using the ARTIC protocol for epidemic surveillance including Ebola, Zika, COVID-19 and Mpox.
• Genomic surveillance: Enables large-scale generation of genome sequences for pathogen monitoring, with SARS-CoV-2 primers used to generate an estimated 18 million genome sequences.
• Wastewater sequencing: Facilitates sequencing from environmental samples for surveillance of endemic pathogens.
• Pandemic preparedness: Supports rapid primer scheme generation for emerging pathogens to scale up genomic surveillance efforts globally.

Methodology:

PrimalScheme uses a greedy algorithm to find primers for tiling amplicon generation across multiple reference genomes.