Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification DOI Creative Commons
Mengfei Peng,

Morgan L. Davis,

Meghan L. Bentz

et al.

Viruses, Journal Year: 2025, Volume and Issue: 17(4), P. 584 - 584

Published: April 18, 2025

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used whole genome SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess improve the performance Illumina NovaSeq, Oxford Nanopore Technologies MinION, Pacific Biosciences Sequel II platforms in identifying lineage assignment. NovaSeq produced highest number reads bases, depth coverage, completeness consensus genomes, stable mapping coverage across open reading frames genome, consistent assignments. The long-read had lower yields, depth, limiting qualified sequences assignment variant identification. However, implementing proper quality controls on sequence data overcame these limitations achieved assignments all three platforms. advancements library preparation technology likely enhance expand effectively addressing current analysis. By merging unique advantages both short- methods, we can significantly genomic provide insights into strategies other RNA viruses, pending further validation. may lead precise tracking viral evolution support policy decisions.

Language: Английский

Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification DOI Creative Commons
Mengfei Peng,

Morgan L. Davis,

Meghan L. Bentz

et al.

Viruses, Journal Year: 2025, Volume and Issue: 17(4), P. 584 - 584

Published: April 18, 2025

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used whole genome SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess improve the performance Illumina NovaSeq, Oxford Nanopore Technologies MinION, Pacific Biosciences Sequel II platforms in identifying lineage assignment. NovaSeq produced highest number reads bases, depth coverage, completeness consensus genomes, stable mapping coverage across open reading frames genome, consistent assignments. The long-read had lower yields, depth, limiting qualified sequences assignment variant identification. However, implementing proper quality controls on sequence data overcame these limitations achieved assignments all three platforms. advancements library preparation technology likely enhance expand effectively addressing current analysis. By merging unique advantages both short- methods, we can significantly genomic provide insights into strategies other RNA viruses, pending further validation. may lead precise tracking viral evolution support policy decisions.

Language: Английский

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