Improved sub-genomic RNA prediction with the ARTIC protocol.

ABSTRACT: Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2's replication, pathogenicity, and evolution. Recent sequencing protocols, such as the ARTIC protocol, have been established. However, due to the viral-specific biological processes, analyzing sgRNA through viral-specific read sequencing data is a computational challenge. Current methods rely on computational tools designed for eukaryote genomes, resulting in a gap in the tools designed specifically for sgRNA detection. To address this, we make two contributions. Firstly, we present sgENERATE, an evaluation pipeline to study the accuracy and efficacy of sgRNA detection tools using the popular ARTIC sequencing protocol. Using sgENERATE, we evaluate periscope, a recently introduced tool that detects sgRNA from ARTIC sequencing data.

SUBMITTER: Baudeau T 

PROVIDER: S-EPMC11417393 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature