Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny.

ABSTRACT: This study proposes a novel approach to studying severe acute respiratory syndrome coronavirus 2 virus mutations through sequencing data comparison. Traditional consensus-based methods, which focus on the most common nucleotide at each position, might overlook or obscure the presence of low-frequency variants. Our method, in contrast, retains all sequenced nucleotides at each position, forming a genomic matrix. Utilizing simulated short reads from genomes with specified mutations, we contrasted our genomic matrix approach with the consensus sequence method. Our matrix methodology, across multiple simulated datasets, accurately reflected the known mutations with an average accuracy improvement of 20% over the consensus method. In real-world tests using data from GISAID and NCBI-SRA, our app

SUBMITTER: Fiam RN 

PROVIDER: S-EPMC11199993 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature