CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes.

ABSTRACT: Phylogenetics has played a pivotal role in the genomic epidemiology of severe acute respiratory syndrome coronavirus 2, such as tracking the emergence and global spread of variants and scientific communication. However, the rapid accumulation of genomic data from around the world-with over two million genomes currently available in the Global Initiative on Sharing All Influenza Data database-is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2 and compactly stored

SUBMITTER: Ferreira RC 

PROVIDER: S-EPMC10131274 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature