Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.

ABSTRACT: Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer mismatches overlapping with primers and predicte

SUBMITTER: Wang MX 

PROVIDER: S-EPMC11282221 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature