Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.

ABSTRACT: Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve the performance of Illumina NovaSeq, Oxford Nanopore Technologies MinION, and Pacific Biosciences Sequel II sequencing platforms in identifying SARS-CoV-2 variants and lineage assignment. NovaSeq produced the highest number of reads and bases, depth of coverage, completeness of consensus genomes, stable mapping coverage across open reading frames in the genome, and consistent lineage assignments. The long-read sequencing platforms had lower yields, sequencing depth, and mapping coverage, limitin

SUBMITTER: Peng M 

PROVIDER: S-EPMC12031342 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature