VPipe: An automated bioinformatics platform for assembly and management of viral next-generation sequencing data

DD Wagner, RL Marine, E Ramos, TFF Ng… - Microbiology …, 2022 - Am Soc Microbiol
Next-generation sequencing (NGS) is a powerful tool for detecting and investigating viral
pathogens; however, analysis and management of the enormous amounts of data …

Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2

AK Gupta, M Kumar - OMICS: A Journal of Integrative Biology, 2022 - liebertpub.com
Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to
stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an …

[HTML][HTML] VirusTAP: viral genome-targeted assembly pipeline

A Yamashita, T Sekizuka, M Kuroda - Frontiers in microbiology, 2016 - frontiersin.org
Although next-generation sequencing (NGS) technology provides a comprehensive means
with which to identify potential pathogens from clinical specimens, simple and user-friendly …

Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: approaches, applications, and considerations for …

I Maljkovic Berry, MC Melendrez… - The Journal of …, 2020 - academic.oup.com
Next generation sequencing (NGS) combined with bioinformatics has successfully been
used in a vast array of analyses for infectious disease research of public health relevance …

Next-generation sequencing in the study of Infectious diseases

NS Zuckerman, LM Shulman - Infectious diseases, 2023 - Springer
Viruses are an important member of the microbiome and have been shown to have an
impact on human health and disease. Next-generation sequencing (NGS) is one of the …

[HTML][HTML] ViralFlow: a versatile automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variant detection

FZ Dezordi, AMS Neto, TL Campos, PMC Jeronimo… - Viruses, 2022 - mdpi.com
The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2
(SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance …

Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 whole-genome sequencing initiative …

EA Smith, KG Libuit, CJ Kapsak… - Microbial …, 2023 - microbiologyresearch.org
The capacity for pathogen genomics in public health expanded rapidly during the
coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did …

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

T Hu, J Li, H Zhou, C Li, EC Holmes… - Briefings in …, 2021 - academic.oup.com
In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia
outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and …

Next-generation sequencing technologies in diagnostic virology

L Barzon, E Lavezzo, G Costanzi, E Franchin… - Journal of Clinical …, 2013 - Elsevier
The data deluge produced by next-generation sequencing (NGS) technologies is an
appealing feature for clinical virologists that are involved in the diagnosis of emerging viral …

[HTML][HTML] Next-generation sequencing: A promising tool for vaccines and other biological products

S Nellimarla, P Kesanakurti - Vaccines, 2023 - mdpi.com
Next-generation sequencing (NGS), also known as high-throughput sequencing (HTS), is a
commonly used term to represent a set of DNA sequencing technologies that have been in …